Miguel/Johto

A woman is shown cooking while she speaks to an Aipom on her shoulder, telling it to go and wake up her son, Miguel. Aipom rushes down the corridor into Miguel's bedroom. All of the Pokémon living at the house are waiting patiently for him to wake up and there is a billiard cue at the rear end of his bed. One of Miguel's jackets is neatly hanging on his bedside. More Pokémon are shown, eagerly waiting for Miguel to wake up. Aipom tries to nudge him awake, and the other Pokémon try as well. Miguel finally wakes up dreary, however, Lickitung soon sorts that. He heads downstairs and greets his mother who makes a funny comment about his hairstyle. Miguel then picks up his skateboard and tells the Pokémon to get ready to play.

Meanwhile, at Professor Elm's research center in New Bark Town, Professor Elm mentions the battle in Kanto, possibly the one between Edge and Robyn. He then focuses on the three Poké Balls on his desk that hold the Johto starter Pokémon. Hoothoot flies over leaving a view of what seems to be Miguel's playroom. Now he is fully dressed and playing billiards. He is listening carefully to DJ Mary's Pokémon Song Hour. As the song is playing, he gets every ball in a pocket. The Template:Wp crackles then dies down, and Miguel is now cross.

He then notices a shady figure in the backyard creeping around in the shadows. He jumps out of the window and confronts the figure calling him a thief and being very annoyed that his favorite song had been interfered with. The figure tells Miguel that he is mistaken, and that his name is Joey. However, Miguel tells his Aipom to attack the boy's Rattata with Scratch. Joey then points up towards the tree where a Murkrow is residing peacefully along with a backpack and an antenna. Joey says it is his backpack which he was supposed to be taking to the Professor.

Miguel shoots up the Poké Ball of Aipom at the tree, telling it to lower down the items. Miguel welcomes Joey, but as he's about to leave, he gets cross with Joey, telling him to give him a recorded version of the show he missed. Joey spends the night, and the next day, they head off for Professor Elm's laboratory so that Joey can deliver important documents that were inside his backpack. Joey explains to Miguel that his backpack contains important documents which he needs to deliver to Professor Elm at Professor Oak's request. Wanting to meet Professor Oak, Miguel decides to tag along.

On the way through downtown New Bark Town, they encounter a Bird Keeper that is scamming Trainers by challenging them to capture all his Pokémon in less than a minute. Instead of keeping honest track of the time, however, his Hoothoot just cries whenever a Trainer is about to win. Miguel, unable to resist a challenge, decides to try anyways. Miguel starts the challenge and calls out the Bird Keeper when he tries to get his Hoothoot to end the game early.

The crowd dissipates, and Miguel realizes his backpack is missing. Joey deduces that because Miguel's backpack is filled with Poké Balls just like his, the thief must have mistaken Miguel's backpack for Joey's and taken it in error. Miguel and Joey head for Professor Elm's lab in search of the thief. Meanwhile, a mysterious character sneaks into Elm's lab, lurking in the shadows and hanging from the ceiling.

When Professor Elm isn't watching, the boy drops down from the ceiling and snatches a Poké Ball containing a Totodile from the table. As the boy is making his escape, Miguel and Joey are trying to enter the lab, so Professor Elm mistakes Miguel for the thief. Miguel chases after the thief, and Aipom fights the thief's Sneasel. Miguel notices on the table that one of the three Poké Balls is missing, and sees that the Cyndaquil inside one of the other Poké Balls is upset that Totodile is missing. As his backpack full of Poké Balls was stolen earlier, Miguel is sympathetic to having a Pokémon friend taken away, so he offers to fight together with the Cyndaquil. He releases it from the Poké Ball and they give chase to the thief. Meanwhile, the Team Rocket Elite Trio is gloating about having stolen Joey's backpack, but to their dismay, they discover it is Miguel's, which does not contain Professor Oak's important documents. Frustrated, one of the members tosses the bag aside, and the Poké Ball containing Miguel's Poliwag rolls away into a river.

The thief escapes from Professor Elm's lab, with Miguel chasing closely behind. Miguel uses Cyndaquil's fire power to contain the thief within a ring of fire, demanding that he return his backpack and return Totodile to Professor Elm. Before the thief can respond, however, Ken interrupts, revealing that it was him who took Miguel's bag, expecting it to be Joey's, which had Professor Oak's important documents inside.

Ken challenges the thief and Miguel to a battle in an attempt to steal Professor Elm's Totodile and Cyndaquil from them. Despite a type disadvantage, Totodile is able to defeat the Ken's Elekid, since the thief taught it Frustration after stealing it from Professor Elm.

Sometime later, a policeman confronts Miguel about the charred lawn, which was damaged by Cyndaquil's fire attacks. Joey explains to Miguel that Professor Elm's hip was injured during the altercation with the thief, and that he had to go to the hospital. The policeman says that the thief who stole Totodile attacked from behind and that Professor Elm, his assistant, and Joey didn't see the perpetrator clearly.

Miguel is taken to the police station to compose a composite image from his memory of the thief. He accurately depicts the boy's hair color and body type, but deliberately adds incorrect facial features. He explains to Joey later that he wants to track down the thief himself, without the help of the police, so he gave them a deliberately incorrect composite to slow them down.

As they are discussing the thief, Professor Oak visits Miguel and Joey's campsite. He asks Miguel if the perpetrator was carrying a Pokédex, which causes Miguel to recall the boy hiding one from Cyndaquil's flames. Professor Oak explains that he only made three new Pokédexes, but one had gone missing three days ago, leading him to believe that Professor Elm's Totodile and his Pokédex were both stolen by the same thief. Miguel asks about the capabilities of the Pokédex, and then asks if he may have one of the remaining two. Despite Miguel's begging, Professor Oak refuses to give him a Pokédex, explaining that he only gives them to Trainers that he trusts, whereas he does not know Miguel at all.

To toughen his Pokémon up, Miguel starts them on a rigorous physical training regime, forcing them to run several laps a day. When it begins to rain during a training session, Joey's Rattata falls off a ledge and into a river, and Miguel jumps in after it to rescue it. He rescues Rattata, but is unable to get out of the river himself until Professor Oak's Ledyba saves him.

Afterwards, Professor Oak scolds Miguel for over training his Pokémon, which results in Miguel begging him for the Pokédex again. When Professor Oak asks him how he feels about his Pokémon, Miguel replies that they are not just friends or comrades to him, but partners united by the same goal. Impressed, Professor Oak gives the Pokédex to Miguel. When Miguel mentions his search for his backpack, Professor Oak reveals that he found it by the river earlier, with Miguel's Pokégear and Poké Balls intact (except for his Poliwag's). With renewed vigor, Miguel continues on his search for the thief, whose name is revealed to be Martinez, when Miguel notices it stitched on the inside of his glove which he picked up earlier.

At the New Bark Town General Hospital, Professor Elm is sad that he is injured, but his assistant says the real problem is that someone broke into his lab. The assistant says that at least the Egg they had wasn't stolen. Suddenly, Miguel calls them with his Pokégear and says that Martinez may have stolen Totodile, but with his Cyndaquil, he will catch Martinez. Professor Elm and his assistant are shocked to realize that Cyndaquil has been taken too.

Meanwhile, Joey returns Miguel's Pokémon to Miguel's mother, who says that Poliwag is missing. Joey calls Miguel and informs him, and Miguel sets out to find Poliwag. He fails to find Poliwag, so he decides to stay on Martinez's trail. Meanwhile, Martinez sees his wanted poster and does a double take.

In Violet City, a thief steals Earl Dervish's package and escapes on his Donphan. Miguel is buying a rice cake, but when the thief passes by, his rice cake gets covered in dirt. Enraged, Miguel chases after the thief. Earl asks Miguel to recover his bag for him. Miguel continues chasing the thief and says that all the thief needs to do is buy him a new rice cake. The thief orders Donphan to attack, so Miguel retaliates by having Aipom use Double Team. This causes Donphan to get confused and crash into a wall, defeated.

To thank Miguel, Earl buys him a huge stack of rice cakes. Earl then tells Miguel that Professor Elm's assistant is coming to Violet City. Meanwhile, Professor Oak and Professor Elm are having a conversation about Miguel. Professor Oak says he is worried, because Miguel is even more hotheaded than Edge.

Back in Violet City, Miguel says that he needs to get some results or Professor Elm's assistant will yell at him for taking Cyndaquil. He asks the thief if he has seen Martinez, but the thief hasn't. Luckily for Miguel, a nearby girl has seen him. She tells Miguel that Martinez is at Sprout Tower. Inside the tower, Martinez gets a call on his Pokégear saying that whether or not he can evolve Totodile is up to his skills.

Outside the tower, Miguel wonders why it is called Sprout Tower, which is when he reads the signpost explaining the legend of the 100 foot tall Bellsprout. He then proceeds to sneak into the tower through a window. He finds a lot of machinery inside the tower, almost getting hit by a gear. Suddenly, a bunch of Sages appear out of the blue, thinking that Miguel has come to train in Pokémon combat. They say that they must shave Miguel's head bald. Miguel says he likes his hair how it is, and that he only came to catch a thief. The Sages, however, try to get Miguel to join by force. They attack him with their Bellsprout, slicing off the front of Miguel's hair. This enrages Miguel, and he has Aipom attack them. The sages have their Bellsprout form a tower and use Reflect.

Miguel checks his Pokédex and sees that Bellsprout is skinny and quick. He begins to wonder if they even have a weak spot. The sages ask what formation Miguel would like for the final attack. Miguel tricks them into making the Bellsprout form a tower and has Cyndaquil use the fire on its back to attack the Bellsprout. The sages let him up to the second floor, finding another Sage. The Sage says the second floor is another training floor. He describes Martinez to the Sage, and the Sage points to Martinez, who is standing in the doorway. Miguel tells Martinez to stop, but Martinez has Totodile use Slash, causing the stairs under Miguel to fall. Aipom helps Miguel hold on to the staircase.

Cyndaquil fights Totodile in an attempt to get it back to Professor Elm. After an exchange of the basic attacks, Scratch and Tackle, Miguel seems to have the upper hand and tells Martinez to return the Pokémon he stole. When Martinez refuses, Miguel says that if he were just about to return a stolen Pokémon, he wouldn't have taken it to begin with, and then shouts that since he promised to get Totodile back, he intends to keep it no matter what. The two then use the Water and Fire-type moves Water Gun and Ember, with the water attack putting out Cyndaquil's flames. Martinez admonishes Miguel, saying that Fire can't beat Water regardless of his feelings, as such an outcome is predetermined by its basic element.

Miguel then yells to Martinez that if that's what he thinks, he'll show what courage can really do, and orders a Smokescreen from Cyndaquil, and in the panic tries to persuade Totodile to return to Professor Elm's side, but instead it bites him. Miguel, shocked, angrily asks whether it really wants to stay with Martinez. Martinez tells him that it seems to, and adds that only a weakling would resort to such a cheap shot. Miguel tells Martinez to shut up, but he replies that he's just telling the truth, and Totodile wants to stay with him to become stronger.

The banter is quickly interrupted, however, as Cyndaquil's smoke from earlier set off a set of traps the Sprout Tower Sages created, and though the two Trainers are able to avoid the first few traps, they get pushed into a tight spot when a massive metal ball starts to roll down the stairs they are on. With the staircase torn by Totodile's Slash attack, Martinez knows that there's nowhere to run, but then also adds that since these were for training purposes, their two Pokémon should be able to help. Cyndaquil and Totodile whisper to one another, and the former begins to set the iron ball on fire with its flames, after which the two Trainers figure what it's trying to do, and Martinez eventually orders an Ice Punch, shattering it and saving them both.

With the danger out of the way, Miguel tries to thank Totodile, but finds the two vanished. A good distance away, Martinez remarks that there were unexpected circumstances, but Totodile has nevertheless evolved into Croconaw, thus completing his mission.

At the Pokémon Association headquarters in Goldenrod City, Bill is discussing with the Pokémon Association about the Gym Leaders in the Kanto and Johto regions, specifically Sabrina, Lt. Surge, Koga, and Giovanni, who are suspected of involvement in Team Rocket's illegal activities, and how the Fuchsia Gym and the Viridian Gym have been empty since the absence of Koga and Giovanni. Bill is about to recommend how to prevent the same thing from happening when he is interrupted by one of the members of the Pokémon Association who says that to accuse without evidence wasn't right, and tells Bill to first repair the Pokémon Transporter before worrying about anything else.

Meanwhile in Violet City, Miguel is leaving Sprout Tower and talking about how he didn't manage to catch Martinez, before thinking about how he and Cyndaquil did not work as well as Martinez and his Totodile. Miguel then asks Cyndaquil if they should stop trying to get Totodile back as it is attached to Martinez or if they should continue to try and nab him. However, this means that Cyndaquil has to go up against his buddy, so Miguel decides to give Cyndaquil sometime before making a decision. He then lies down to get some rest, when suddenly a herd of Oddish passes by, and Miguel looks them up on his Pokédex, before complaining that his beauty sleep is gone.

Suddenly, a Bird Pokémon flies over him, and Miguel hears a Trainer in the distance. It turns out to be Falkner, whom Miguel has forgotten, and only remembers him after Falkner mentions how he had helped in the drawing of the thief at Professor Elm's lab. After speaking to Falkner for awhile, Gold finds out that Falkner was undergoing Pokémon training to take over the Violet Gym by passing the Gym Leader Initiation Test, and how it was his life's goal. Miguel thinks about his goals too, which are to find his Poliwag and catch Martinez. Suddenly, Falkner gives Miguel a push, telling him to duck as a gust of wind blows past. The culprit is soon revealed to be a wild Skarmory who, according to Falkner, has been causing unrest in the area. The Oddish in the area start jumping around, trying to escape from the Skarmory.

Falkner then engages in battle with the Skarmory, saying they might need fire to weaken the metallic Pokémon. Miguel then calls out Cyndaquil, but worries that his billiard cue will not be able to launch Cyndaquill high enough to hit the Skarmory. After seeing the Oddish, he gets an idea and catches one of the wild Oddish, before ordering it to jump into the air with Cyndaquil on it to transport it into the sky. When Cyndaquil is high enough, it uses Ember, allowing Falkner to capture the Skarmory. After the battle, Falkner thanks Miguel, and Cyndaquil decides to stay with Miguel for the moment. Falkner then offers Miguel to participate in some intensive training with him, but Miguel declines, saying that he still has something he needs to do first. After a few encouraging departing words, Miguel and Falkner split up. Meanwhile, Bill is on his way to meet Falkner when he sees Miguel with a Pokédex in his hands, but after reminding himself not to get distracted, he continues on to meet Falkner to pass him the Gym Leaders Inauguration Examination Notification letter.

At the Pokémon Center in Violet City, Professor Elm's assistant contacts Professor Elm, explaining that he wasn't able to find Miguel. Professor Elm replies that he had tried calling Miguel on his Pokégear, but to no avail and it would have been better if the Pokémon Transporter was working. Professor Elm's assistant asks if it would be okay to pass something so important to someone as reckless as Miguel, to which Professor Elm replies that in order for it to hatch, it is best to place it around other Pokémon. Professor Elm's assistant then takes out a Pokémon Egg.

Miguel attempts to cook lunch. He tastes it and feels that it has to be cooked more, and asks Cyndaquil to do so, but Cyndaquil ends up burning the meal. Miguel sighs that his lunch is gone, and that he is still unable to find Martinez and Poliwag. Miguel looks at his Pokégear and finds out that they're at the Ruins of Alph. Miguel then sees a girl and runs up to her immediately, asking her if she is lonely sightseeing by herself and inviting her for a cup of tea. The girl introduces herself as Bugsy, and that she is actually a guy, leaving Miguel embarrassed. Bugsy explains that he wasn't really here to sight-see, but to search for his missing companions.

Bugsy explains that he was part of the relic expedition in Johto and that his companions were checking out the ruins, but they had suddenly lost contact. Bugsy then asks why Miguel is at the ruins, and Miguel replies that he was searching for his missing Poliwag. Bugsy is shocked and wonders if some bad guys stole it, but Miguel highly doubts it. Bugsy then says that there were reports of missing Pokémon at the Famous Fishing Zone. Suddenly, Aipom pipes up, as it heard sounds coming from the other side of the wall. Miguel then attempts to burn through the wall with Cyndaquil and succeeds, ignoring Bugsy's pleas of not destroying Johto's historical site. Miguel argues back by saying that Bugsy's companions might be on the other side of the wall, and seeing that Cyndaquil had created a hole in the wall, goes through the hole, with Bugsy on his trail.

Miguel sees a mysterious code on the wall, and Bugsy guesses that it is the story of the legendary symbol Pokémon written 1,500 years ago, and that it might be proof that mankind coexisted with Pokémon back then. Miguel says that it would be more important to search for Bugsy's companions first, to which Bugsy apologizes and agrees. As Miguel and Bugsy prepare to search, they're tied up in string. The culprits are revealed to be the Team Rocket Elite Trio, who plan to get the Symbol Pokémon for themselves. Cyndaquil struggles to get free, but it is in vain. Ken calls out his Elekid and his Elekid aims its electricity for Miguel, ready to be shot out if Miguel retaliates.

Miguel then pretends to admit defeat, while Aipom behind him uses its tail to take out Oddish's Poké Ball. Oddish blinds the Team Rocket trio with Flash and while Ken, Al, and Harry are blinded, Miguel quickly unties Bugsy and they attempt to make their escape, however, the symbols on the wall start coming off, revealing themselves not to be explanations of the Symbol Pokémon, but the Symbol Pokémon themselves. Oddish's Flash from earlier had awakened them. Miguel and Bugsy make a run for it. Afterwards, Ken, Al, and Harry regain their sight, and they plan a trap for Miguel and Bugsy.

Meanwhile, Miguel and Bugsy have lost the Unown and realize they are lost themselves. They then hear a cry for help, and the two run towards the direction of the voice. However, a spider web blocks their way. This web, unlike the web from earlier that had tied Bugsy and Miguel up, had a stickier substance and was used for ambushing people. Bugsy suggests they go the other way, but the other way is blocked by a spider web too. Soon, Miguel and Bugsy are surrounded as they cannot advance because of the spider webs, and the Unown are behind them, ready to attack. Just as Ken, Al, and Harry gloat over their victory, smoke surrounds them, and when the smoke clears, all of the Unown are stuck to the spider webs. The Unown zap the Team Rocket trio out of commission before going back into their slumber. After Miguel apologizes to the Unown, the two make their way out of the ruins.

After Bugsy's companions are out, Bugsy thanks Miguel, saying that the ruins would be a new course of sightseeing because of the discovery of the Unown. Miguel and Bugsy then part ways. At that same moment, the Team Rocket Elite Trio are still stuck in the ruins, trying to figure a way out, when they're contacted by their current leader, who berates them for failing again.

Miguel reaches Route 32 to find Poliwag's Poké Ball. There, he meets up with Wilton, who then informs him of the sneak thief who'd been stealing Poké Balls off many fishermen right after they captured the Pokémon. Soon, though, before the man could finish his explanation, a shadowy figure deftly snatches the Poké Ball he was holding, and an angry Miguel uses his billiards pole to hit the pilferer straight in the jaw. It is then revealed as a wild Granbull that had a dislocated jaw it needed to have fixed, and Miguel's shot did just that. The two then order the calmed Pokémon to give back the Poké Balls it took, and among the dozens it spat, Poliwag's was among them. After Miguel and Aipom rejoice their tearful reunion, Wilton offers his phone number for Miguel to register, all while thinking that the boy's performance with his billiards pole was as impressive as his niece's adroitness in handling a fishing rod.

Miguel then happily walks about (musing that Wilton was one strange guy), before formally introducing Cyndaquil and Oddish to Poliwag. On his Pokégear, he informs the good news to Joey and Professor Elm, while noting that since the transportation devices aren't working, he'll just have to keep Poliwag on his team for now. A figure then jumps out of the grass, to whom Miguel asks "what" he is, before he introduces himself as one of Professor Elm's assistants, who wants to leave a Pokémon Egg with Miguel for safekeeping. Professor Elm then informs Miguel of his failed attempts at having it hatch, which he deems an important project, due to the fact that no one has yet seen an egg hatch. Miguel flips out and asks just what his research has to do with anything, but he replies that a stimulus of being in a more active environment might be able to speed up the process.

Meanwhile, Martinez visits Kurt's house in Azalea Town, where an overworked Kurt soon hands him a Heavy Ball crafted from the Black Apricorn he handed to the old man earlier. Soon, Miguel too reaches the town and sees an Apricorn tree, from which he picks (what he thought to be) "an edible fruit," and Kurt's granddaughter gets a laugh at him before telling him that the Apricorns are meant for creating special Poké Balls with. Miguel then mocks the practice and says it's a waste, to which Kurt cavorts in rage and tells him that before Poké Balls were mass-produced at factories, the Poké Balls made by his family for generations were the norm. He then adds that with Miguel's level of discipline, the beginner Poké Balls sold at Poké Marts are probably the most fitting, but this time, Miguel barks in a rage and tells him that if he can't use one of his oh-so-magnificent Balls properly, he'll work as Kurt's apprentice for the rest of his life. Kurt then orders Miguel to pick one of those fruits so he can craft a Poké Ball for him, and the boy yells just why he has to pick the Apricorn in the first place.

Soon, with a Friend Ball in his hands, he promises that with the Poké Ball he obtained, he'll catch a friend for the little girl, who then requests that it be a Teddiursa, which she has heard is around the mountains nearby. Miguel complains that she should've picked a safer environment to catch one from, only for a wild Ursaring, the evolved form of Teddiursa, to attack them from behind. They then find themselves on the run, only to bump into Martinez, who Miguel suspects stole the Heavy Ball he's holding, but the girl corrects him and says that Kurt made one for him. Miguel is a little peeved that the old man would find him unworthy of his Poké Balls and give a handmade one to Martinez, and swiftly changes his target to the Ursaring. After Aipom is ordered to attack, Martinez calls him a flout for trying to steal his target, but Miguel tells him that it's a fair game, but finding Aipom, Croconaw and Sneasel's attacks to be of annoyance, the enraged bear attacks the girl, whom Miguel saves, but when her favorite Pokémon, Teddiursa, jumps in, Miguel ends up spraining his ankle.

Miguel clutches his leg in pain, as the Ursaring and Teddiursa loom over him. Maizie tries to catch his attention, as the Ursaring lunges at them, claws bared. Miguel tells the girl to run, as a Sneasel intercepts the attack. From the attack, Ursaring's paws are frozen solid, as Martinez informs Miguel that the Ursaring came back for a trophy, much to Miguel's contempt. Suddenly, the ice surrounding Ursaring's arm begins to thaw out, as Martinez realizes that it is using Fire Punch to thaw the ice. As this happens, Miguel questions Martinez's motives, wondering whether he is truly protecting Maizie out of the goodness in him. Teddiursa then lunges at Aipom, as Miguel warns his Pokémon not to get distracted by its cute looks. Whilst Teddiursa and Aipom flail in mid-air, Miguel attempts to capture the wild Pokémon. However, the Poké Ball merely bounces atop Teddiursa's head, much to Miguel's surprise. He wonders why the capture was unsuccessful, proceeding to try again with the same outcome.

Miguel is furious, believing that Kurt gave him a faulty Poké Ball. However, Martinez corrects him, stating that it was his fault. Gold tells him to be quiet, as Martinez explains that this is more proof of his inexperience. Martinez then states that this is the perfect opportunity to use the special Poké Ball Kurt made for him. He apologizes to Miguel, preparing to claim the Ursaring as his. However, Martinez is knocked off balance by Aipom, who was thrown by Ursaring. As a result, Martinez loses his grip on the Poké Ball, which clatters to the ground. Martinez glares at Miguel, who states that Aipom's actions were not his fault. The three of them are forced to run away from the advancing Ursaring and Teddiursa, but find themselves trapped on the edge of a cliff. Tears begin to well in Maizie's eyes as she reveals that she disobeyed her grandfather's instructions by venturing up to the mountains. However, Miguel consoles her and asks that she trust his judgment. Miguel asks Martinez to teach him the special technique in catching, to which Martinez complies. Martinez explains that while speed and timing are crucial, a capture can be guaranteed if a Poké Ball is aimed at its target's vital spot, where its life energy is most concentrated. In this case, Miguel needs to aim for the center of Ursaring's belly and the crescent on Teddiursa's forehead.

As Miguel prepares to hurl his Poké Ball with his stick, Martinez asks which Pokémon he will use it on. Miguel does not reply, and instead hurls the Poké Ball in such a way that it rebounds off surrounding rocks. In doing so, he knocks Martinez's Heavy Ball back into Martinez's hand and the Friend Ball into his. Miguel comments that they are now ready to capture both Pokémon. The two of them hurl both their Poké Balls simultaneously at their opponents, resulting in a perfect capture. Maizie is ecstatic at their accomplishment, as Miguel brags about his involvement. Martinez instead states that the Ursaring is the least of his problems now, before running off into the distance. Miguel comments that he will never understand what is going on in Martinez's head. Miguel then gives the Teddiursa to Maizie, as they proceed to leave the mountaintop.

At the Slowpoke Well, several Team Rocket Grunts are scavenging Slowpoke Tails from the Slowpoke. However, they are interrupted by the arrival of Martinez, who smirks. Meanwhile, Miguel and Maizie arrive at Kurt's house and immediately realize something is out of the ordinary as the water will not turn on. Kurt arrives at the Slowpoke Well, and is surprised that all of the Team Rocket Grunts have been bound and gagged.

Maizie happily approaches her grandfather, but Kurt simply berates her for disobeying his instructions. She sincerely apologizes to him, prompting Kurt to relent, stating that she is safe and that is all that matters. Miguel asks Kurt what transpired here, to which Kurt confirms that they were in this state when he arrived. Miguel senses a presence approaching them, but relaxes when he discovers it is only Bugsy. Bugsy informs Miguel why he came to the Slowpoke Well, asking Miguel whether he was responsible for this. Miguel denies this, prompting Bugsy to wonder who was really responsible. Maizie expresses her sympathy for the Slowpoke, as Miguel uses Aipom to make the Slowpoke yawn. As the Slowpoke opens its mouth, water comes rushing out from the well, as Miguel reveals that this was part of his plan, based on a legend that the yawn of a Slowpoke brings water. Miguel then departs from Azalea Town, wondering whether Martinez could have been responsible for the apprehension of Team Rocket, due to the fact that Ursaring claw marks were found at the scene. Miguel wonders what Martinez's ulterior motive is, commenting that it will be exciting to find out what his true goal is.

A Farfetch'd is cutting firewood for the Charcoal Kiln worker. He congratulates his Pokémon on its work, as an eerie mist floods through the area. The worker comments that Ilex Forest has been getting increasingly misty over the past few days. Before he can leave, he realizes that Farfetch'd has run off yet again. The worker calls out to his Pokémon, then a voice emanating from within the forest tells him to leave immediately. He instantly becomes clammy with fear, unsure of what he has heard. The voice repeats its warning, prompting the worker to scream loudly. Miguel arrives at the entrance to Ilex Forest, commenting that he needs to venture through here in order to catch up to Martinez. Miguel comments that the forest is creepy looking, but states that as long as he follows the path, he will not encounter danger. He berates Martinez for not thanking him for his help, commenting that he needs to find out who Martinez really is. However, as Miguel is lost in thought, his Pokégear notifies him that there is no data in his present location.

Miguel sighs in disappointment, confirming that he is indeed lost. However, Miguel wonders whether something mysterious is taking place here, as the forest path only heads in one direction. As Miguel is walking blindly through the forest, he trips over the body of an unconscious Farfetch'd. Subsequently, Miguel again trips, this time trip the body of the worker. Miguel tries desperately to get the boy's attention, but realizes that he is in a poor condition. He resolves to carry the injured worker on his back as he skates through the labyrinthine forest. He looks back at the injured Farfetch'd, commenting that its injuries are not of the normal kind, and even its leek got destroyed by whatever attacked them. Miguel wonders whether the assailant used teeth or knives in his attacks, as a cold chill runs down his spine. He is instantly snapped out of his thoughts by this, and proceeds to leave the nearby area. However, his Pokémon slowly become adversely affected by an ominous presence, before Miguel realizes the worker and his Farfetch'd are possessed.

He throws them to the ground, as a Gastly appears around the possessed duo. Miguel comes to the conclusion that it was the Gastly that was the cause of all this chaos, as Farfetch'd is commanded to attack him. In turn, Miguel retaliates by sending out Aipom, who is swiftly defeated. Miguel realizes that they cannot win whilst the two are possessed, and begins to flee. As Miguel runs, he seeks refuge behind the Ilex Forest shrine, as the possessed worker and Farfetch'd search for them nearby. Miguel states that he could win easily if it were a regular Pokémon battle, but since they are possessed by Gastly, there is little he can do. He notices Poliwag walking behind the Gastly, and runs out of the clearing to rescue it. Miguel calls out to his Pokémon, and catches it just in time as a possessed Ariados, Houndour and Delibird surround him. The Houndour lunges at Miguel with Bite, which is deflected by Cyndaquil's Smokescreen. However, as Miguel is preoccupied, Poliwag is incapacitated by Gastly.

Miguel calls out to Cyndaquil, only to see him faint at the hands of Houndour. He does the same with Oddish, telling her to use Growth, before she is knocked out by Ariados. Miguel's attention is then averted to Aipom getting attacked by Delibird, and wonders why these Pokémon are faster than his own. He then realizes his disadvantage, and notices a figure lurking in the thick mist. Miguel attacks with Cyndaquil's Ember attack, which is countered by Houndour's Flamethrower. As Cyndaquil falls unconscious to the ground, a mysterious figure emerges from the mist. The figure then tells Miguel to stay away from Ilex Forest.

Miguel realizes that the mysterious figure is the leader of the mutated Pokémon. Miguel states that fighting him in his current state will not be an easy feat, but neither will be getting the injured out from the area. He apologizes to the figure for trespassing, but proclaims that his idle threats will not stop him. Miguel sends Aipom hurtling at the figure, telling the Pokémon to show the figure what he is made of. As Aipom repeatedly pummels the figure, Miguel uses this temporary window to attempt an escape with the injured worker. However, Miguel finds himself surrounded by the four mutated Pokémon, as the figure chides him for not finishing their battle. The figure asks Miguel whether he would like to become one of his guards, to which he realizes that the figure was responsible for the brainwashing of the worker and his Pokémon. Miguel states that the figure's actions are despicable, and resolves to make him pay for severely injuring his comrades.

The figure and Miguel stare at each other for several moments, as the figure commends Miguel on his show of bravery. The figure then states that Miguel deserves a present, as Delibird hands him a gift-wrapped box, which promptly explodes in his face. Miguel instantly realizes that they have been tricked, as Gastly and Houndour attack Miguel's Poliwag and Oddish. This sends Miguel hurtling to the ground, who promptly calls to Cyndaquil for assistance. The figure laughs, explaining that he fell for his "jack-in-the-box" surprise, preparing to ask him how it felt. However, Miguel is nowhere to be found, and the figure postulates that he used his Cyndaquil's Smokescreen attack to escape. As he looks down at the unconscious body of the worker, the figure realizes that Miguel wants them to chase after him. However, the figure is undaunted and wonders whether they are seeking refuge in the trees. The figure uses his Ariados to illuminate the surrounding area, as Miguel realizes that he is done for. Miguel wonders why someone so powerful is lurking around in Ilex Forest, as a sudden noise alerts him to the situation taking place.

He realizes that the figure is using his Delibird to uproot the trees with Headbutt. Miguel tries to think of something before they are found, as their tree begins to topple to the ground. Suddenly, a light illuminating from the Ilex Forest shrine catches the figure's attention. This prompts him to order his Pokémon to give up the search, proclaiming they have more important things to tend to. However, his Pokémon are caught off guard by a falling object resembling Miguel. However, the figure is surprised when it turns out to just be Miguel's jacket stuffed with leaves. The real Miguel emerges from the bushes behind the figure, attempting to use Oddish's Mega Drain on Ariados. However, Ariados intercepts this attack by firing spiderwebs from its back, proceeding to bind Miguel. Due to Miguel's intervention, the light from the shrine fades away, as the figure states that they have lost their chance. As the figure prepares to leave, a bound Miguel tells the figure to take off his mask and fight him fairly. The figure merely laughs, stating that even then he would be outmatched, much to Miguel's chagrin.

Later, Miguel gets Aipom to pull apart the webs binding him. He thanks Aipom for freeing him, explaining that they need to get everyone out of the forest as soon as possible. Miguel notices his Pokémon cowering, and realizes that they were frightened of the figure's mask. He reassures them, proclaiming that the figure will not get away with his plans. This statement makes Miguel's Pokémon instantly cheer up, as they emerge from the forest undaunted. As Miguel carries the unconscious worker, he hopes that this statement will come true. As Miguel recuperates at the Pokémon Center, Professor Elm inquires on his condition. Miguel explains that he is fine, but the worker he saved is still unconscious. Professor Elm reveals that a thorough analysis of the material the figure was wearing is a crucial clue to unraveling this mystery. He tells Miguel to keep an eye on the issue too, as Miguel states that the figure's attitude is somewhat reminiscent of Martinez's attitude. Meanwhile, Martinez is informed by Lance that Miguel has come into contact with the Masked Man, and that he should keep a close eye on Miguel.

At the Violet Gym, Falkner is appointed the new Gym Leader of the Violet Gym. The Pokémon Association Chairman asks Bill to fix the Pokémon Storage System in return for appointing Falkner. Falkner expresses concern that his appointment may have caused problems for the Pokémon Association, but Bill assures him that it is not his fault and mentions a friend of his that is taking the Gym Leader exam as well. The Pokémon Association member hands Falkner the Zephyr Badge and explains the duties of a Gym Leader, while Falkner wonders where Miguel is.

Miguel arrives at the outskirts of Goldenrod City and comments on the beauty of the city at night. Because he has no money, he chooses to rest for the night outside of the city. Then, a Smeargle appears and paints Miguel's face, waking him up. Miguel chases after the Smeargle, using Aipom's tail to trip it, and Cyndaquil's flame to stop it in its tracks. His attempt to finish it off with Oddish fails when Smeargle covers his face with paint. Hiro sees Miguel and offers him a spot on his show, "Pokémon Talent Round-Up". Miguel eagerly accepts the offer, happy to make money and to have a chance to meet DJ Mary. While in the Goldenrod Radio Tower, Miguel sees the Smeargle that attacked him and attempts to go after it. He ends up interrupting an interview between Mary and Whitney.

Meanwhile back in New Bark Town, Joey tries to listen to the radio, only to hear Miguel and Whitney arguing. The show is taken off the air as Hiro scolds Miguel and Whitney for potentially ruining it. A staff member barges in and tells Hiro that they are getting calls by the hundreds, which Hiro assumes are all complaints. However, the staff member explains that the calls are all positive, who are all entertained by the back and forth between Miguel and Whitney, and many ask for the two Trainers to battle. Miguel and Whitney agree to the fight, and Hiro decides to create a special about the match.

The match between Miguel and Whitney follows Pokémon Battle race rules, following a path from Goldenrod City to the Route 37 road sign, with battles being allowed as well. Since the program is sponsored by Miracle Cycle, Miguel and Whitney must use bicycles from their shop, causing Miguel to complain about being unable to use his skateboard. Instead, he removes the handlebar from his bicycle and puts it on his skateboard, allowing Miguel to use his skateboard and advertise for Miracle Cycle.

The race begins and Whitney instantly orders her Miltank to use Rollout on Miguel. Hiro tells the vans to move into position, so they can keep up with Miguel and Whitney. However, van three is unable to go any further because of an odd tree in the way. Miguel is quickly closing in on her. Her lead is ruined completely by an odd tree that is blocking the path. Angered, Whitney commands Miltank to use Rollout on the tree to little effect. Miguel, who wants to prove he's better than her, tells Cyndaquil to use Ember on the tree, also doing little. Miguel sends out Aipom, Oddish, and Poliwag to attack the tree next. However, the tree only reacts to Poliwag's water attacks.

Suddenly, a Rhydon appears and Whitney attacks it using Miltank, with little effect, and Rhydon then kidnaps Whitney. DJ Mary pleads for someone to save Whitney. The race is called off and all vans are sent after Rhydon. Before Miguel can go after Rhydon as well, he notices the tree shaking. He tells Poliwag to use Water Gun on the tree again, and the tree shrinks down to reveal itself as a Sudowoodo. Sudowoodo had been pretending to be a tree because it was being chased by Rhydon. Miguel tells Sudowoodo that it needs to stand up for itself and decides to teach it how to fight.

Miguel catches Sudowoodo, and sends it out as close as possible to Rhydon by using his pool cue. Sudowoodo emerges from the Poké Ball and sucker punches Rhydon, defeating it instantly. Despite the race being called off, Miguel declares himself the winner, since he moved the tree out of the way and saved his opponent. After getting autographs from DJ Mary, Miguel heads to the Goldenrod Game Corner.

Miguel is playing pool at the Game Corner, and the people around him remark on his incredible skills. Then, they see a ball curve and give the situation a reality check as the wrapping comes off Aipom's Poké Ball, which Aipom is running inside of. Miguel is then kicked out. Outside, Miguel receives a call on his Pokégear from Professor Elm. Miguel tells the professor about his team: Cyndaquil, Aipom, Oddish, Poliwag, Sudowoodo, and his Egg. Professor Elm tells Miguel to keep a close eye on the Egg.

Right after Miguel goes to sleep in the woods on the outskirts of Goldenrod City, a Gligar snatches his Egg. Aipom tries, unsuccessfully, to wake Miguel. Then, the loyal Pokémon chase Gligar. When Aipom tries to attack Gligar, it uses Poison Sting, causing Aipom to fall. Then, Gligar kicks Poliwag, who has just jumped out of the water. Pretending to be a tree, Sudowoodo catches Gligar. Then, Cyndaquil uses a powerful Ember, but the Egg starts to sizzle. Gligar flies over to a tree to eat the Egg, but Oddish lands on Gligar's head. Unfortunately, that makes Gligar headbutt the Egg, creating a crack in the shell. Then, pieces of the Egg fly off, and a Togepi appears.

Apparently, Gligar still wants to eat the newborn. But Togepi uses Double-Edge, then Metronome. Metronome comes out as a beam of energy that hits Gligar. Suddenly, Miguel wakes up. At the Pokémon Center, Miguel is having a conversation with Professor Elm via the computer. Professor Elm is very proud of Miguel, until he sees Togepi playing pool with Miguel's cue stick and his Poké Balls, playing a card game, and rolling dice, just like Miguel.

On the southern outskirts of Goldenrod City, Miguel recalls Professor Elm telling him to take the Togepi to the Day-Care Couple at the Pokémon Day Care. After a bit of walking in a field, a Magby, Smoochum, Cleffa and Igglybuff jump out of some bushes. Then, an old lady tells Miguel old to get them back.

After that's done, Miguel is at the Day Care, with the ex-escaped Pokémon and the Day-Care Couple. The Day-Care Man thanks Miguel and tells him a bit about Togepi: two unknown Pokémon were there. Then, they disappeared, and an Egg was found. With the short story over, the Day-Care Lady asks Miguel to train there, which Miguel accepts. Meanwhile, the Day-Care Man calls Jasmine.

Inside the Pokémon Day Care, the old woman and Miguel look at some books. Miguel sees a picture of Edge and his Pokémon. Afterwards, Miguel enters another room. Upon entering the other room, the old woman puts bars in, trapping Miguel, who finds angry Pokémon inside the room. Miguel notices that all the Pokémon are elite fighters. A second into the battle, he is being chased by a Tauros. Dodging more attacks, he has Cyndaquil use Smokescreen, and Togepi use Metronome. Metronome becomes Leer, which hits an Ekans. Cyndaquil then uses Ember on a Donphan, who deflects it with Rollout. Following the instructions of the Day-Care Lady, Miguel tells Poliwag to use Water Gun. The attack hits Donphan and sends it flying.

In Ecruteak City, Jasmine walks toward the Day Care. However, an earthquake hits and the ground underneath Jasmine's feet breaks, causing her to fall in. Back at the Day Care, a Primeape uses Cross Chop on Sudowoodo. Sudowoodo counters with Mimic. Noticing that Sudowoodo is taking more damage than Primeape, he has Oddish use Sunny Day. With Sunny Day's effects, Miguel orders Cyndaquil to use Ember, whose powers become enhanced by Sunny Day. In midst of the attack, Cyndaquil evolves into Quilava as Ember defeats Primeape with ease.

The Day-Care Man hears a message on the radio: Ecruteak City has been hit by a major earthquake. The Day-Care Couple starts to worry for Jasmine. But then the Day-Care Lady realizes that *someone* can help. In Ecruteak City, standing on boulders, Miguel recalls the Day-Care Lady telling him that he's mastered the training and giving him a King's Rock. They also asked him to look for Jasmine.

Meanwhile, Martinez is Flying via his Murkrow over the ruins of Ecruteak City. Inside the Tin Tower, Jasmine tells Amphy to shine a light. Outside, Amphy's light is seen by Miguel, who then hurries towards the tower.

Back inside the tower, Jasmine finds Martinez standing over her. When Miguel runs into the room, Martinez is carrying the unconscious Jasmine. Martinez tells Miguel that he's going to help Jasmine, but Miguel doesn't believe it, so Martinez puts Jasmine in Miguel's arms. Miguel looks at the statue of Ho-Oh, then runs off to the exit. Suddenly, boulders and pieces of wood fall towards Miguel, but Martinez's Ursaring pushes the landslide back. Ursaring then uses Fury Swipes on the wall, which causes it to brake. Amphy runs out carrying Jasmine, however, the exit is suddenly covered by rocks. Martinez returns Ursaring to its Heavy Ball.

Quilava ignites its fire, and Miguel thanks it for the light. Martinez angrily yells at Miguel, because fire eats up oxygen, therefore Quilava's flame is put out. Then, a landslide rushes forward, so Miguel has Quilava use Flame Wheel on the ceiling. This does not work, and the former land gives everyone a small space between the mud and the ceiling. Martinez tells Miguel to send out his Water-type Pokémon, because water will pull up underground water, which will let them escape. Miguel sends out Poliwag, who is holding the King's Rock, and Martinez sends out his Croconaw. Martinez says that the maximum amount of water that Poliwag can use is too small, but then Poliwag evolves into Poliwhirl. Martinez tells Miguel to trade using the Pokédex. Miguel subsequently trades Poliwhirl for Martinez's Seadra as the tower is completely filled with mud. Then, water shoots out of the tower, along with Martinez, Miguel, Croconaw, and Miguel's newly-evolved Politoed. After escaping the Tin Tower, Martinez realizes that the earthquake was caused by a trained Pokémon. Martinez also thinks about the ice in the Tin Tower.

Outside the Tin Tower, Sham, Carl, and Team Rocket Grunts appear. The Team Rocket Grunts send out Cubone, Drowzee, Ledian, and a Ninetales to attack Miguel and Politoed. Martinez tells Miguel that Team Rocket caused the earthquake. Carl then recognizes Martinez, and tells the Grunts to attack Martinez too, but the Pokémon that try are knocked out by Miguel and Quilava. Carl's giant Piloswine appears, and attacks Miguel and Martinez. When Miguel tells Politoed to use Water Gun, Politoed does nothing.

Martinez lets Miguel battle the Team Rocket Grunts, while he battles the Piloswine. Piloswine chases Martinez, who is Flying on his Murkrow to dodge. However, with the power of liquefaction and Politoed's Whirlpool, Piloswine is defeated. Then, Carl notices that Miguel has defeated the Team Rocket Grunts's Pokémon. Sham then says that their mission is complete, so they can retreat. After Team Rocket retreats, Miguel and Martinez trade back their Pokémon. Following this, Miguel challenges Martinez to a battle.

Meanwhile at the evacuation shelter, some doctors are taking care of Jasmine. She tells them about Miguel and Martinez rescuing her, but they do not believe her. Elsewhere, in Ecruteak City, Miguel and Martinez prepare for their battle, with Miguel stating he'd been looking to battle him ever since they first met.

After a heated match, and an excellent display of their Pokémon's moves, Martinez's Pokégear rings with a voice telling him to head to the Lake of Rage because of suspected activity. Martinez announces that he must end the battle quickly in order to leave for the Lake of Rage, and sends out his Tyranitar. It appears that its Sandstorm has ended the battle, however, it is revealed that Togepi had buried its head into Tyranitar, using Double-Edge. Tyranitar falls as a result of the powerful attack, which surprises Martinez. Miguel looks around at his exhausted Pokémon and announces that Martinez has won the battle, but that he would win the next time and tosses Martinez his Pokégear. Martinez warns Miguel to stay out of his way and turns to leave. However, he stops and decides to tell Miguel about Ho-Oh. He tells him that the disaster in Ecruteak City was a result of Team Rocket attempting to call upon the Legendary Pokémon. Martinez says that they were testing to see if attacking the Tin Tower would force Ho-Oh to return to its nest. Martinez then reveals that his purpose is to wipe Team Rocket out, by any means necessary, explaining why he stole Totodile. He leaves with Croconaw and Sneasel. Miguel watches him leave, and decides that Martinez shouldn't be fighting Team Rocket alone, and runs after Martinez, calling out to him that he is coming with him.

At the Lake of Rage, Martinez announces that his mission has begun. Elsewhere, Miguel wanders around, disappointed that he has lost track of Martinez. Suddenly, many Gyarados come out of the water. Everyone runs away from the powerful Pokémon, but then Miguel spots Martinez running toward the lake, whom Miguel follows. He starts to talk to Martinez, but Martinez pushes him away. Then, a Gyarados plows forward, crushing the earth where Miguel was standing. Martinez then shows Miguel what's happening: the Magikarp are suddenly evolving into Gyarados. Martinez also shows Miguel his Pokégear, which has nothing but static. Martinez reveals that radio waves are causing the static on the Pokégear and causing the Magikarp to evolve. Then, Martinez flies away on his Murkrow.

Miguel starts to fight the Gyarados. He sends out Politoed, who uses Double Slap. But there are so many Gyarados, and the lake is filled with Magikarp, so more and more Gyarados appear by the second. Meanwhile, Martinez is trying to find the source of the problem instead of fighting the many Gyarados. However, despite their best efforts, neither Miguel nor Martinez can locate the source of the radio waves.

Meanwhile at Professor Elm's laboratory, Joey and Professor Elm are trying to contact Miguel, but are unable to get through because of outside interference.

Back at the Lake of Rage, another Gyarados appears, but it is red instead of blue. Suddenly, Miguel and Martinez's Pokégears have an even worse connection, which means that the red Gyarados is the source. The way to end the radio waves is to capture it. So Politoed uses Whirlpool and Martinez's Murkrow uses Pursuit. To finish it, Martinez captures the Gyarados in a Lure Ball and the radio waves stop, causing the Pokégears to have a connection and the Gyarados's minds of their own again. Afterwards, Miguel and Martinez start to argue, but suddenly, the Masked Man appears.

After seeing the Masked Man, Miguel immediately has his Politoed use Dynamic Punch, but Politoed's hand is frozen. Then, Miguel himself charges forward, but Martinez pushes him backward and has his Kingdra use Twister so that Miguel can see the ice spikes that were hidden by the mist. Suddenly, Professor Elm calls Miguel on his Pokégear. He tells Miguel that evidence says that the Masked Man is a Gym Leader, and to not fight the Masked Man. However, Miguel is in the middle of doing exactly that.

The Masked Man's Delibird uses Blizzard, creating more ice spikes. The Masked Man says that Martinez can't run away from him like last time. Martinez and his Sneasel seem aggravated. Sneasel then uses Icy Wind. Delibird feints at Miguel, then punches Martinez in the face. The Masked Man steps on Martinez's hand to hold him where he is. Miguel finds out that the Masked Man kidnapped kids nine years ago, and one of them was Martinez.

Martinez prepares to send out a Pokémon, but the Masked Man tells Martinez that if he does that, he'll kill Miguel since his Delibird's arm is frozen to make an ice spear. The Masked Man tells Martinez that he's gone weak. However, Miguel knows the truth and tells the Masked Man that Martinez is strong and that he has seen Martinez's strength many times. Then, Quilava throws Delibird off its feet. Martinez and Sneasel get a bit farther away from the Masked Man. The Masked Man sends out his Houndour and his Shiny Ariados.

Quilava and Sneasel launch a combined attack of Flame Wheel and Icy Wind against the Masked Man's Ariados and Houndour. However, the Masked Man's Pokémon osuddenly disappear, and Miguel, Quilava, and Sneasel are hit by a barrage of surprise attacks afterwards. The Masked Man then suddenly appears beside Martinez, and taunts him by mockingly asking if Roberta survived making their escape, which angers him.

Losing his cool, Martinez commands a Quick Attack from Sneasel, but neither it nor a Rock Smash succeed in even making one hit. Miguel tells him to cool down and think straight, but when Martinez sees the Masked Man apparently fleeing on his Delibird, he has Sneasel freeze Miguel's feet to get him away. Martinez then gives chase with his Murkrow, but is overwhelmed as the Masked Man further taunts him by telling him that Martinez played right into his trap. However, Martinez has other plans, and then, after launching a barrage of Pecks from Murkrow, he uses the red Gyarados he captured earlier to bring all the Gyarados that were forcibly evolved, and launches a powerful Hyper Beam.

Meanwhile, Miguel is still being chased by Houndour and Ariados, but soon after having Aipom put them out of commission with a clever Double Team maneuver, is shocked to discover that the entire lake, and the Gyarados with it, has been completely frozen and then finds Martinez unconscious. Furthermore, to his amazement, a giant chunk of ice hits Martinez and his Sneasel head-on, and leaves them sinking to the bottom of the lake. Miguel calls out for Martinez and yells for him to snap out of it, but is then hit by a barrage of ice shards as the Masked Man announces that it's his turn. Grinning with ecstasy, the Masked Man deems them nothing but powerless braggarts, and tells Miguel that it's time to join his friend. Miguel mutters that the battle was between the two of them, not Martinez, but the villain bounces right back by saying that anyone who betrays him or becomes an obstacle will perish. Miguel yells that it's not anyone's right to manipulate and restrain anybody, but before he can react, another large chunk of ice falls right before his head, and he, too, is sent plummeting to the bottom of the lake as he begins to scream.

Miguel awakens on one of the Whirl Islands and expresses his relief at being alive to Aipom. Still, he wonders where he could be, recalling that he was last at the Lake of Rage fighting the Masked Man with Martinez, for whom he then frantically searches. Miguel finds Martinez alive and awake, resting, as he says, until Miguel got up. Martinez states that they should not move about too much as they are wounded. Martinez recalls the two of them having been rescued from drowning by something big and shadowy whose extraordinary flames warmed them; Miguel only vaguely recalls feeling as though something were watching over him. But the two boys's musings are interrupted when they see that they have stumbled upon a herd of crouched Sandslash, whose species they cannot identify at first. The spiky beasts roll menacingly toward the two; Miguel is slowed by his missing shoe and, as he has lost his bag, he cannot retrieve his Pokédex. Miguel and Martinez then send out their entire teams (except for the red Gyarados that Martinez caught at the Lake of Rage). Martinez's Croconaw knocks out one of the pursuers and reveals its identity.

Meanwhile, Lt. Surge, who is aboard a ship headed for the same island, is looking through a pair of binoculars when he spots the boys, who have managed to escape the Sandslash. "*Ahoy, below!*" calls Lt. Surge, his arms full of the boys' missing possessions as he floats in the air above. As he comes down, he announces, to the bewilderment of Miguel and Martinez, that he has a red Gyarados in a Poké Ball. After he drops the items, Miguel pores over them excitedly as Lt. Surge jokingly demands gratitude. As Miguel begins clumsily to oblige, Lt. Surge, in all seriousness, asks them for any information they may offer about the Masked Man. Martinez, though he would happily answer, first asks Lt. Surge whether he came in on the ship docked nearby. As Lt. Surge affirms it, the ship is suddenly lifted into the air as Lugia emerges.

Bayley, Rosita and Wilton are aboard Wilton's ship, which, along with the S.S. Aqua, is borne aloft by Lugia's Psychic power. Someone aboard the S.S. Aqua calls to Lt. Surge below for help as Miguel announces that every ship in the area is levitating in a similar fashion. Martinez guesses that psychic power of such magnitude must be the work of Lugia. Suddenly, Lugia fires an Aeroblast at the crag which Martinez, Miguel, and Lt. Surge are standing on. The three avoid the attack, but then Lugia plunges the S.S. Aqua back into the sea, causing a tidal wive to form. In an instant, Martinez calls out Murkrow and flies off, despite Miguel's objections and Lugia's repeated blasts.

Lt. Surge is revealed to have escaped the wave by using his levitating Magneton and he then finds that Miguel has escaped as well by the same method. Lt. Surge expresses his annoyance, but Miguel callously makes himself Lt. Surge's responsibility, stating that he has neither a flying nor a surfing Pokémon. As Martinez flies out of sight, Lt. Surge dodges an Aeroblast with Miguel's warning. In return for Lt. Surge saving Miguel's possessions, Miguel agrees to tell him everything that he knows about the Masked Man.

Miguel reveals that they fought the Masked Man twice, and his strategy relies heavily upon ice: he uses previously unheard of techniques and froze an entire lake in seconds. Lt. Surge privately reflects that the Gyarados he found there was frozen and that when he fought the Masked Man, his adversary did not even attempt the use of ice. Miguel leaves off this narrative, having revealed all that he knows and the more pressing issue is dealing with Lugia.

Meanwhile, Wilton, who has been released, along with Bayley, Rosita, and his ship from Lugia's psychic clutches asks the two girls if they are okay. However, Bayley, looking skyward, only answers that the Pokémon is the same one she saw over Cerise Island: she says that it was said to have vanished into the Western skies after a battle with Lance. Rosita's Pokédex beeps. Bayley suggests that this is because of the Resonance System: when three Pokédexes, in the possession of their rightful owners, draw close to each other, they beep. But Lugia's blast interrupts, which causes Wilton's boat to break in half and start sinking. Meanwhile, Rosita recalls that Professor Oak told her of two other Pokédex holders in Johto.

Meanwhile, Martinez is still grasping Murkrow's airborne talon, reflects that the Sandslash were hiding from Lugia, but wonders why Lugia is going berserk. Suddenly, he spots Wilton's boat, and releases himself from Murkrow and lands on his Croconaw, he heads for the doomed vessel. Miguel spots the same scene; he and Quilava promptly leap from Lt. Surge's force-field and head for the boat. He and Martinez at once put forth their hands to help Rosita, who chides them for a pair of delinquents. Their Pokédexes all beep at once: the very three Pokédexes, they understand, given by Professor Elm and the professor's three starter Pokémon as well have been reunited. Another Aeroblast hits the water and the severed ship leaps into the air. Once it has hit the water again, Martinez orders Croconaw to ready itself to leave, but Miguel tells him that all three starters are prepared to fight the Diving Pokémon and that they ought to be given a chance.

With a frightened Rosita as witness, Miguel and Martinez quarrel aboard half of Wilton's fishing boat after surviving one of Lugia's attacks. Martinez starts to depart, ordering his Croconaw to come along, but Miguel assures his rival that the starter Pokémon of all three Pokédex holders are prepared to fight the menacing Lugia and that the trainers, regardless of their opinions of each other, should trust their Pokémon. Quilava, Croconaw, and Bayleef attack as one, their elemental powers barely deflecting another of the Diving Pokémon's blasts. The boys quarrel further over emotional style and Rosita loudly questions Professor Oak's choice of Pokédex holders, to which Miguel accuses her of being prissy.

Nearby, Lt. Surge floats above the sea with the help of his three Magneton. He notes that Lugia's blasts, not being the result of any perceptible build-up of energy, are rather the results of Lugia's breaths, for which phenomenon he dubs the attacks Aeroblasts. Facing another of these, Surge realizes that if his Magneton were to take the strike, they would drop him. He then glances across the waves at Martinez, noting that he must know a way to stop Lugia's attacks.

Back on half of Wilton's boat, Martinez has proposed that Lugia be drawn into the sea, where it will be unable to gather air for its terrifying technique. At close range, Martinez proposes, brute force can be inflicted on Lugia's head and wings. However, he knows that Miguel lacks a Flying Pokémon and will be of no help in the fight. Martinez tells Miguel to stay put with the three starter Pokémon, and then summons his Murkrow, while Rosita sends out her Natu. However, as they take flight, they knock Miguel into the sea. Martinez and Rosita toss him a life-preserver just before his Pokégear rings. Wilton has called with an important bit of news and is floating right behind Miguel, barely holding on to the other half of his boat, which contains a number of Poké Balls. A tidal wave interrupts their conversation.

Completely submerged, Miguel silently ponders his predicament until he spots a wild Mantine, who is apparently cowering because of the blasts. Miguel swims over to it, but then, his waterlogged body slackens pulling the rope on the life-preserver taut and then snapping the rope. The worried Martinez and Rosita hear a dull rumbling from the sea. Suddenly, Miguel emerges with his new Mantine, which is supported by Wilton's school of Remoraid, two of which bite Miguel's cue such that he can hold on as if to a glider and the rest face the other way in order to keep Mantine and Miguel aloft with their jets of water. Miguel tells Martinez and Rosita that they will have to watch him defeat Lugia by himself.

Miguel continues gliding towards Lugia and orders the school of Remoraid to veer right and then fire at their target. On the boat, Martinez watches in astonishment and Rosita cheers. It appears that the Remoraid have wounded Lugia with their combined Water Guns, but instead, they only enraged it. The Diving Pokémon whirls about and knocks Mantine, Miguel, and the Remoraid out of the sky and onto the sand below. Rosita observes this and Martinez notices that, although Miguel did not bring Lugia down, he did force its mouth open with his cue stick.

Martinez has Croconaw paddle the boat over to Miguel, all while Lugia looms overhead. Miguel, hurt, gently taunts Martinez and Rosita for being bystanders and introduces Quilava to his new teammate, Mantine. Suddenly, the Legendary Pokémon's shadow hovers over them. As Lugia descends, the three are knocked backwards; unable to fire an Aeroblast, Lugia attempts instead to crush the trainers and their starter Pokémon with its wings. Croconaw, Quilava and Bayleef resist the onslaught and, in doing so, evolve together, into their final forms.

When Rosita asks why Bayleef evolved into Meganium, and Martinez replies that he heard that when Pokémon of similar evolutionary levels spend time together, their natural competitiveness accelerates growth. However, Miguel interrupts Martinez's explanation, insisting that it should wait until Lugia has been defeated, and asks whether Martinez, who has spoken in the past of a Pokémon's "vital spot", could spot Lugia's. Martinez says that its vital spot is its forehead and Miguel has to hit it right between the eyes.

Tossing a Poké Ball, Miguel misses the spot, and declares the he can't aim well without his cue. When the Poké Ball hurtles back, Rosita kicks it back again and hits Lugia right between the eyes. In a flash of light, the Diving Pokémon is gone and the Poké Ball sits on the beach. Miguel recovers his cue and congratulates Rosita, but Martinez notices that Lugia isn't inside the Poké Ball. They think about how and when Lugia could have escaped. Rosita finally realizes that it must have flown off in the flash of light. Miguel stomps about in frustration when Rosita remembers the tracking system on the Pokédex, which can track the energy of any Pokémon the Pokédex holder has encountered.

Rosita then asks Miguel and Martinez if they had heard of the feature before, but they say nothing and pretend to know how to use the system, Miguel looks over Rosita's shoulder as she activates the system on her Pokédex and mimicks her actions. Miguel apparently offends their new acquaintance by telling her that she is not merely a "motor-mouthed prissy girl." Rosita then introduces herself at last, but Miguel ignores her, deeply involved as he is waiting for the tracking system to track Lugia. Ignoring both of his companions, Martinez climbs up the island's crag and discovers a cave which, by virtue of the tracks before its entrance, he deems to be Lugia's lair.

Rosita recounts a legend that the four Whirl Islands are connected by tunnels and states that these would be a suitable hiding place for a gigantic Pokémon. Martinez also sees signs of a struggle, and he and Miguel suppose that Lugia might have been attacked before they encountered it. Rosita states that it would explain its rampage, but suddenly the tracking system crashes on all three Pokédexes. Realizing that it isn't likely that all three would fail at once, Miguel states that the only explanation is that Lugia has already been captured by someone else.

Meanwhile, the S.S. Aqua is safe and sound again, swiftly cutting through the waves. A sailor aboard is relieved that he made it out of the attack, when Lt. Surge suddenly bursts through the door of the ship's control room, alive and unharmed. Just as Lt. Surge begins to reflect on his adventure, a letter comes in at the ship's bridge, which is a summons for Lt. Surge and all the other Gym Leaders to appear at the Pokémon Association headquarters in Goldenrod City.

Back on the Whirl Islands, Martinez speculates that someone could have struck Lugia with a Poké Ball immediately before Rosita did. Martinez then brings out his Murkrow, guessing that whoever attacked Lugia in the cave is the culprit and that the entire fight that they had with the Legendary Pokémon was a trap. Despite Rosita's objections that he should at least speak to Professor Oak and Professor Elm before chasing Lugia's captor, Martinez flies off clutching Murkrow's talon. Miguel assures Rosita that Martinez would not call the Professors under any circumstances and, in spite of his old habit of warning Martinez not to try to handle everything on his own, thinks well enough of this departure as he and Martinez have a common enemy this time. Rosita begins to wonders what Miguel could mean by that, but remembers Bayley and Wilton.

Suddenly, she gets a call from Professor Oak on her Pokégear. Professor Oak states that he is aware of the unusual events near Cianwood City and has called to check on Rosita. Rosita tells him about everything that has happened to her lately, including the part about losing Bayley. Oak informs her that there is a meteorological crew on the way, and he will tell them to look for Bayley. He also needs her to go to the Indigo Plateau, and says that he was also going to ask Miguel to go, but has been unable to reach him and could be anywhere. However, Rosita reveals he is standing right next to her.

Meanwhile, Martinez flies high above the island chain and lands on the southernmost isle, which is the only one that he and Miguel have not visited. Its crag houses a whirlpool and at the back of which is a roaring waterfall. Touching down, Martinez sends out Gyarados, Kingdra and Feraligatr and orders them to use Whirlpool, Waterfall and Surf, respectively. Using Feraligatr, Martinez sails over the calmed pool and steps through the parted fall into what appears to be a man-made chamber. From the darkness comes a voice affirming the place hidden to all except those with three Water-type Pokémon with a precise combination of talents. Lance then steps forward, congratulating Martinez on reaching the chamber.

Miguel and Rosita are making their way towards the Indigo Plateau on Typhlosion and Meganium, respectively. After a brief quarrel involving Miguel's potatoes, they arrive to a large queue at the Indigo Plateau entrance. Miguel retrieves Typhlosion and jumps the queue using his scooter, causing Rosita to chase after him. Rosita is stopped by a security guard and told to pay the entrance fee for Miguel, much to Rosita's annoyance. Suddenly, Rosita hears a scream and wonders what Miguel got into trouble for again.

It turns out that a security officer accidentally released three of the entry-registered Pokémon that were being guarded, those being three Yanma which have snatched a mother's baby and are now carrying it around a room. While the other guards attempt to locate the Yanma's trainer, Miguel decides to solve the problem himself. He uses his cue to knock a Poké Ball around the room. The Yanma get dizzy from attempting to dodge the Poké Ball, such that the one holding the baby drops it. Fortunately, Sudowoodo emerges from the Poké Ball to catch the baby and return it to its mother. Before Miguel can brag about his success, he is dragged away by the ear by Rosita. Rosita then receives a call from Professor Oak, who asks to remind Miguel of his mission, but Miguel claims he knows already. With that, they enter the stadium just as it begins to host the Gym Leader exhibition matches.

During the opening ceremony, the battle stage expands, and the Magnet Train line emerges from the void, with the train itself eventually entering the stadium too. Backed by a fervent atmosphere, the Gym Leaders of both Kanto and Johto emerge from the train to opposing sides of the stage, and are introduced to the crowd. The draw for the exhibition matches then takes place, with Apricorns representing the lots to draw from. Erika and Pryce, being the Gym Leader team captains of their respective regions, face each other last, so the other seven leaders of each region pick a different-colored Apricorn to determine their opponents.

* Brock draws Jasmine.
* Misty draws Whitney.
* Blaine draws Clair.
* Sabrina draws Bugsy
* Janine draws Falkner.
* Lt. Surge draws Morty.
* Robyn Oak draws Chuck.

The order of the matches is then randomly determined, and the Pokémon Association Chairman officially inaugurates the series of exhibition matches. As the Gym Leaders retreat to their seats, the Chairman knows that Professor Oak's chosen Trainers are also helping them out with the real purpose of this congregation.

Later, high up in one of the audience stands, Miguel and Rosita watch on as Misty gets ready for the next Gym Leader exhibition match against Whitney. Miguel and Rosita struggle to spot any obvious signs of evil among the Gym Leaders. Thinking back to their call with Professor Oak earlier, this very event came about after Miguel submitted evidence of his encounter with the Masked Man to Professor Elm, who later discovered that the traces found on the evidence were of materials used to create Badges. This evidence was later passed to Oak and the Pokémon Association Chairman in top secret, and it was decided by the Pokémon Association to host a Gym Leader exhibition event just before the real tournament at the Indigo Plateau. As Miguel fought the culprit earlier, he was instructed to observe the Gym Leaders's battling styles, and Rosita was to accompany him and prevent him from rash actions.

In the present, Miguel decides to move to a lower audience stand, and disappears into the crowd. Soon, Rosita finally locates Miguel, who, after commenting on the Gym Leaders, declares his unease at the thought of an evil presence among a tournament meant for Pokémon lovers. He is determined not to let such a person spoil it.

During the final battle of the event, Erika battles Pryce, and throughout the battle, Miguel's suspicion is raised after comparing Pryce's battling with that of the Masked Man. Aipom suddenly alerts Miguel to someone spying on him and Rosita, and the two give chase to the culprit. They end up inside the Indigo Plateau's central control room. Miguel approaches someone in the room, and on a closer look, sees that the person has fainted. A voice states that they now have control of the Indigo Plateau. Miguel and Rosita turn to see Carl and Sham, the two that Miguel recognizes as behind the Ecruteak incident. Miguel tries to confront them, but finds that he cannot move. Carl and Sham proudly announce their leader's intentions by projecting the Masked Man's battle with Ho-Oh, captured live from a pair of binoculars, onto a screen in the central control room.

Miguel and Rosita, bewildered that the Masked Man appears to be somewhere else, and not among the Gym Leaders as they were told, then realize that Ho-Oh is the one being attacked. Carl and Sham boast that not even the Legendary Pokémon can escape capture by the Masked Man. They then switch off the live recording, declaring that the Masked Man's arrival is imminent, and that Team Rocket will be resurrected once more. With that, they throw down their Team Rocket jackets and put on their half-masks.

Miguel, still unable to move, suddenly realizes that it is because of Roar. He and Rosita then find themselves surrounded by several Houndoom and Persian. Aipom finds a way to release Politoed from its Poké Ball, and Politoed instantly puts its opposition to sleep with Hypnosis. However, Sham's Slowking snores loudly to create solid air blocks, and Carl's Magcargo breathes out fire while asleep. Rosita has her Cubone swat away Slowking's Snore while Miguel has Politoed counter Magcargo's Fire attack with Water Gun. Both soon struggle with their opponents.

Sham wastes no time with their opponents' struggle, and begins hacking the central controls. Miguel and Rosita eventually have Parasect and Oddish's combined Giga Drain knock out Magcargo and Slowking by sending them crashing towards their Trainers, and as a result, Oddish evolves into Gloom due to the experience she gained. By this time, the alert sirens sound. Despite being grabbed by the collar by Miguel, Carl gloats at his successful mission before fainting. The monitors then state that the Magnet Train lock is being released.

At the Magnet Train station serving the Indigo Plateau, two guards who are watching the Magnet Train suddenly become horrified when the train's lights flicker on to reveal a large number of masked Team Rocket Grunts inside. The guards quickly rush to alert their boss, but the Team Rocket Elite Trio zap them unconscious and enter the train.

Unable to find a way to abort the release of the Magnet Train's security, Miguel decides to go back to the stadium for help, but soon finds that he and Rosita are trapped inside. They call out Typhlosion and Arcanine to burn the door down, but the door remains intact. Rosita finds that her Hitmonchan's Mach Punch doesn't break down the door either. While Rosita thinks hard for another solution, Miguel finds a way to contact the rest of the stadium from the control room.

Miguel's face appears on the big screen over the stadium, much to the Pokémon Association Chairman's fury. The boy manages to warn the audience about Team Rocket's impending arrival and the Magnet Train being hacked, before the big screen is suddenly interrupted to show the Masked Man's battle with Ho-Oh, causing the audience to panic. By then, Rosita has prepared a mix of spores from Parasect, which, combined with Gloom's Sludge Bomb, tear a hole through the door. Just as Rosita and Miguel break free from the control room, the Magnet Train zooms into the stadium once again.

As the stadium audience evacuates, the Chairman, who has come down from the VIP room along with Bill and Carly Oak, tries to call for the Magnet Train system to be fixed. At the next moment, the Magnet Train doors bolt open and numerous masked Team Rocket Grunts spill out. Falkner calls the Gym Leaders into action. Blaine arrives back on stage just in time to join the fight against the grunts. When 15 of the 16 Gym Leaders are lured into the Magnet Train, however, its doors slam shut and the train speeds off into the distance.

By now, Miguel and Rosita are on Mantine and Natu, respectively, looking over the scene of chaos. They hover towards the announcer's box where DJ Mary and Hiro are. They confirm that Miguel's message went through, and that the Gym Leaders went on the Magnet Train before it zoomed off. Rosita knows the Gym Leaders's roles, and that they were tricked into entering the train as a means of diverting attention away from their enemy. A voice duly confirms Rosita's claims. Miguel and Rosita turn around to see that the Masked Man has arrived, with both Lugia and Ho-Oh.

Lugia and Ho-Oh are commanded to use their signature attacks, Aeroblast and Sacred Fire. Miguel and Rosita, on their Mantine and Natu, respectively, dodge, but the attacks cause a blast through a part of the stadium's wall and ceiling, throwing Miguel and Rosita off their Pokémon. They fall right above the part of the stadium whose roof is about to fall on them, fortunately, Sudowoodo shields the two Trainers. The audience are still being evacuated.

Miguel eventually finds out that the Masked Man was also behind Lugia's rampage at the Whirl Islands, and tricked them into thinking Lugia was still wild at the time. Another blast from the two legendaries' attacks strikes another part of the stadium. Miguel and Rosita run, dodging multiple blasts directed at them. Rosita decides that the two should be split apart, thus flies on Natu to face Lugia. Miguel occupies Ho-Oh using Sudowoodo, with Sudowoodo responding to a Ho-Oh attack using Flail while also blinding him with Mud-Slap. The Masked Man calls Lugia to assist, but suddenly feels his neck spasm due to Natu's Future Sight.

The Masked Man responds by morphing into a more mutated version of himself, and jumps onto Ho-Oh, commanding it to trap Miguel and Rosita with a ring of fire. He then proceeds to grab both Kurt and his granddaughter Maizie from the evacuating crowd. The Masked Man states that he requires Kurt to create a Poké Ball to control time. He also contemplates Rosita's use of Future Sight, iterating that she was able to understand the concept of time well, even if for just a few seconds. After praising her, he recalls the goals of the past villainous groups, Team Rocket and the Elite Four, and reveals that his goal is to have complete control of time. As Kurt pretends to not know how the control of time is possible, the Masked Man grabs his granddaughter and holds her in a threatening matter as he surreptitiously steals Kurt's manual, which has data on all types of special Poké Balls.

After he finds the information on the Poké Ball that can surpass time, Kurt mocks him, saying that the manual is worthless without the ingredients for the Poké Ball. The Masked Man then states that he already knows what the ingredients are, and, as he refers to the wings of Ho-Oh and Lugia, his Delibird takes the Silver and Rainbow Wings from the Legendary Pokémon and gives them to him. While he states that he will finally gain control of time, Miguel grows angry over the prospect that Pokémon were being used just as ingredients and materials to the Masked Man. He then demands what Pokémon are to the Masked Man and gets the response that they are mere weapons.

The Masked Man then loses his patience with the conversation and attempts to attack both Miguel and Rosita, but, as Miguel pushes her out of the way, Rosita is unharmed while Miguel takes the hit. Rosita then begs the Masked Man to stop, but is shrugged off as he flies away. As Miguel gets up from the attack he had absorbed, he privately vows to not give up until the Masked Man is defeated. The Masked Man flies on his Delibird towards Ilex Forest, stating that he has finally obtained a "second chance at time".

After the Masked Man defeats the Gym Leaders who attempted to stop him, Miguel stubbornly follows him to Ilex Forest. While on the way, the Masked Man tells Lugia and Ho-Oh to join Will and Karen at their destination. He lands on a mountainous area on his Delibird, and mutters to himself. He is heard by Miguel, who announces his intentions to stop him. The Masked Man taunts Miguel over his previous defeats. Miguel, now with his full team called out, throws a Focus Band to each of them, and retrieves all but Sudowoodo and Aipom.

Aipom, thrown forward by Sudowoodo, uses Agility around the Masked Man, who swats it away. The Masked Man then knocks Miguel back, just as Miguel is about to strike his four other Poké Balls with his cue. At the next moment, the Masked Man sees the Poké Balls roll towards him. Typhlosion, Politoed, Gloom and Mantine pop out. Politoed grabs Delibird and makes a humming noise. The Masked Man goes for Politoed, but Sudowoodo, with Aipom's Agility transferred to it via Baton Pass, holds him back. He calls Delibird for help, but notices that it has fainted along with Politoed due to the latter's Perish Song.

The Masked Man roars, and starts regenerating his lower body with ice. Miguel gets Mantine to propel Gloom skywards. Gloom uses Sunny Day and Miguel throws her a Leaf Stone, evolving her into Vileplume. With a powered-up Flamethrower, while also aided by Vileplume's Solar Beam, Typhlosion melts away the Masked Man's lower body, and Miguel gets the chance to pin him down and shatter his mask. Shocked, Miguel mutters the Masked Man's true identity: the Mahogany Town Gym Leader, Pryce.

Miguel demands Pryce to surrender by holding him at cue-point. However, Pryce spots Edge's Pikachu and Chuchu running by and captures them with his ice body, ordering Miguel to fall back by holding the two Pikachu hostage.

Back at the Indigo Plateau, the remaining Gym Leaders are shocked at the revelation of Pryce's villainy, with Whitney having figured it out due to Pryce being the only Gym Leader missing. Morty, picking up Pryce's abandoned staff, opens it up to reveal a high-tech device that comprises a transceiver and monitor which displays the Tin Tower. Morty realizes that when everyone witnessed the Masked Man earlier while all the Gym Leaders were present, it was actually a remote-controlled dummy manipulated by the staff which Pryce could also monitor through the staff's viewing screen. Whitney adds to the explanation by pointing out Pryce's habit of tapping his staff on the ground; the series of tapping was actually a code that transmitted vocal orders to the dummy, allowing Pryce to control his Pokémon from afar.

Miguel is forced to drop his billiard cue due to Pryce's threat, allowing the latter to attack him while he completes the GS Ball. Miguel is unable to fight back due to protecting Pikachu and Chuchu's Egg, allowing Pryce to escape into time with the GS Ball. Shortly afterwards, Miguel encounters Wilton and the Day-Care Couple, who have escaped from the Team Rocket Grunts. Wilton and the Day-Care Couple hand Miguel a letter from Professor Oak. Miguel is disappointed to not find battle advice, but a letter introducing the other Pokédex holders and their own special skills:

* Edge, who possesses keen battle instinct, is known as the **Fighter**.
* Robyn, who is skilled in training Pokémon to their best, is known as the **Trainer**.
* Bayley, who holds in her the unique heritage of Viridian Forest and her keen connection with Pokémon, is known as the **Healer**.
* Rosita, who had been trained in catching Pokémon since she was young, is known as the **Catcher**.
* Roberta and Martinez, having been specially trained by Pryce, possess keen insight in triggering Pokémon evolution and trading: two effectively similar traits. They hold the titles of **Evolver** and **Trader**, respectively.

An increasingly frustrated Miguel wonders if Professor Oak is asking him to fall back, on the basis that he himself has no particular strength that makes him worthy. However, the Egg in his hands begins to hatch, having been held by him for protection. Wilton realizes that Miguel missed out on a final portion of Oak's message, which acknowledges the abilities of all the Trainers that were given a Pokédex, including Miguel - known as the **Hatcher**. A Pichu hatches from the Egg and jumps onto Miguel's head, and releases its electricity to propel itself and Miguel into the time aurora Pryce left behind, allowing Miguel to chase after Pryce into time.

Later, Pryce returns from the time void and meets up with the other Pokédex holders. When Rosita asks Pryce where Miguel was, Pryce reveals that he managed to trap him in an ice mirror after being constantly pursued while in the Crack in Time. Martinez has Entei free him and Rosita with its flames, but Pryce escapes by jumping into the Ilex Forest shrine.

Miguel apologizes to everyone for being defeated. Martinez attempts to rescue him by reaching into the shrine, only for his hand to get distorted by the time stream. Miguel states that only those who have the Silver and Rainbow Wings will be able to move about the time stream freely. Bayley realizes that the feathers in her hat must be the feathers from Ho-Oh and Lugia that were also used to make the GS Ball. Miguel notices as well, and demands that she give him her hat so that he can be freed. Bayley takes off her hat and tosses it to Rosita, who frees Miguel from his icy prison. Although shocked to find out that Bayley is actually a girl, Miguel thanks her for being courageous enough to take her hat off. With the Rainbow and Silver Wings in hand, Miguel hops onto Raikou's back and jumps into the Crack in Time with Martinez and Rosita following behind on Entei and Suicine's backs, respectively.

As they pass through the time stream, the trio witness various moments from their journey. They quickly come upon moments of Pryce's past to when he was a young man. In a snowy region, a young Pryce watches as his two Lapras fall to their deaths in an avalanche. Pryce notices a crackling sound in his pocket, which turns out to be a Pokémon Egg. The Egg hatches into a baby Lapras, which begins looking for its now-deceased parents in vain. With tears in his eyes, Pryce begs the Lapras to forgive him. Pryce approaches the trio, and introduces them to his Lapras, La Glace.

Pryce states that he intends on changing the past so that La Glace can be reunited with its parents. Rosita questions why Pryce would go to so much trouble for the sake of one Lapras. This angers Pryce, who states that although it might not be important to her, to him it means everything. Pryce lashes out at Miguel and takes the Rainbow and Silver Wings, removing the protection they have from the Crack in Time. Pryce reveals that although he claimed that he considers Pokémon to be nothing but tools, he was actually lying. Pryce states that everyone else is just tools in his grand scheme of bringing back the Pokémon he loves. Pryce commands Celebi to bring him back to the day where he lost La Prus and La Pris.

Miguel, Rosita, and Martinez struggle to move forward. Seeing the moment from when they first met, Miguel apologizes to Martinez for thinking he was a thief. Martinez asks why Miguel continues to fight and wonders if it's because of him. Miguel denies this claim and states that he's fighting for himself. Miguel manages to grab the feathers and hands them to Martinez and Rosita, who he thanks for all the battles they shared together. Miguel leaps further into the time stream to face Pryce once more, leaving Martinez and Rosita behind in the process. Miguel tells Pryce to let Celebi go free. Pryce claims that Miguel has no right to tell him what to do since he doesn't understand how he felt when he lost La Pris and La Prus. Miguel states that he actually does, since he was given the title of Hatcher from Professor Oak and can emphasize with him.

Miguel and Pryce continue battling it out, but Miguel manages to pierce through his ice body with his pool cue. Miguel commands Pichu to attack with Thunder Shock. Although too far away to help, the other Pokédex holders assist Miguel by firing their Pokémon's attacks straight at the defenseless Pryce. The attacks not only shatter Pryce's ice body, but also the GS Ball, releasing Celebi and exposing Pryce and Miguel to the Crack in Time's effects. As Miguel falls unconscious, La Glace immediately flies out of its Poké Ball and into a bright light. Pryce sees that it actually went back in time and reunited with its lost parents. Through Celebi's abilities, Pryce suddenly begins hearing a song and seeing visions of people from his past.

Elsewhere, Wilton expresses disbelief at the Day-Care Couple having known Pryce in the past. The Day-Care Couple explain that years ago, they were friends together with Pryce, Professor Oak, Agatha, and Kurt, sharing a variety of ambitions and love for Pokémon. After Pryce lost his Lapras at the Ice Field, he became bitter and distanced himself from people, eventually becoming the man he is today. The group of friends wrote the song Boy and his Lapras in an attempt to reach out to their friend, but failed to ease his pain. Back in the Crack in Time, Pryce is moved to tears at Celebi's attempt to heal the pain in his heart. Pryce tells Miguel to cherish the time he has with his friends and purposely lets himself fall further into the Crack in Time.

Rosita, Martinez, Entei, Raikou, and Pichu all emerge from the shrine unharmed, much to the relief of the Kanto Pokédex holders. When Bayley asks who hatched Pichu's Egg, Martinez gravely informs her that it was Miguel, who is now lost in the Crack in Time. A moment of silence passes before Robyn Oak apprehends Martinez, arresting him for his earlier thefts. Rosita pleads with Robyn on the basis that they had just lost a comrade, but Martinez assures her that with everything resolved, he is willing to accept punishment for his crimes. Before they can leave, a voice calls out to Robyn and tells him that Martinez can't be arrested because the picture on the wanted poster doesn't look like him at all.

The voice is revealed to an alive and well Miguel, who states that misunderstandings tend to happen. Rosita is shocked to see that Miguel is still alive, but he tells her that she shouldn't just assume that he's dead so easily. Miguel thanks Bayley for her help earlier, only to be shocked to find out that she's older than him as well. Wilton and the Day-Care Couple arrive with the rest of Miguel's team. As Roberta notes Gloom's evolution into Vileplume, Miguel takes the chance to pat her rear, earning a beating from an angry Edge, and the two subsequently comically fight one another, much to the sweat drops of the remaining Pokédex holders, with the exception of Roberta, who's both embarassed by Miguel's actions, and flattered by Edge defending her, and Rosita, who despite Miguel's perverted action, wipes a tear out of happiness for his return.

Meanwhile, Karen and Will watch the commotion from above and note how even the weak become strong when banded together. When Karen wonders what to do without Pryce, they are approached by Bruno and Koga, who suggest that since they are all former villains, they should work together. Karen and Will accept the offer as long as it means that it keeps them entertained.

At the Indigo Plateau, Misty decides to report to Erika via her Pokégear. Since Erika lent her Pokégear earlier to Edge, Edge ends up being the one who receives the call. Misty's feelings for Edge couple with Bayley noticing that Edge is talking to Misty creates an awkward tension in the air. Roberta, fully aware of the tension between them, smugly declares that neither of them had a chance since Edge was "her man", much to their embarrassment. Miguel decides to ease the awkwardness by calling his mother and tells her that he is going to train with Edge. Although Edge is shocked to hear that Miguel actually does want to be trained, he suggests that they go to Mt. Silver since it has powerful wild Pokémon. While on the way, Miguel decides to release Mantine back into the wild, as Mantine had fulfilled its purposes, and Mantine wanted to return to its home, and the two bid farewell to one another, before Edge and Miguel continued towards Mt. Silver.

With the crisis resolved, the damage done to the Pokémon League meant that it had to be cancelled and no winner was announced. Clair reported that she has lost her battle to Blaine, meaning that the Kanto Gym Leaders have won the exhibition match. All the commotion coupled with the new rule that Gym Badges allow one to skip the preliminary rounds of the League means that the Gym Leaders are busier than ever while they deal with challengers. Bill, having learned of Pryce's attempt to control time, begins to incorporate time in his research for improving his Transfer System.