Miguel/Arceus Arise

Three years later after the Battle Frontier incident, Miguel and his Pokémon stand before Arceus. Miguel questions Arceus about how they got into this situation. Miguel commands a Blast Burn from Typhlosion, who fires a powerful flame attack at the Alpha Pokémon. Miguel introduces himself to Arceus and questions why he has to fight it when he was trying to save it. Arceus lets out a powerful roar, which causes Miguel's team to recoil in pain. As Miguel urges his Pokémon to last until Martinez arrives, Arceus begins glowing brightly.

A couple of a weeks ago, Miguel, along with Whitney, ride on top of Typhlosion and Miltank to another location. A hungry Miguel complains and asks if they have arrived at their destination yet. To appease his hunger, Miguel pulls out a Rage Candy Bar and throws one into Whitney's mouth, which causes her to start choking. To dissolve the manjū, Miguel has Politoed shoot a water attack at Whitney, soaking her and Miltank in the process. Angered, Whitney begins attacking Miguel for almost causing her to choke.

Eventually, they enter the Pokéathlon Dome. Inside the arena, DJ Mary and Hirō oversee the events. Upon entering, Miguel gets on his skateboard and attempts to skip through the line. Annoyed at Miguel's antics, Whitney has Smeargle cover Miguel's face in paint and drags him away while apologizing to everyone else. While Whitney continues to drag him away, Miguel begins looking around for someone he was supposed to meet. Miguel complains that Whitney got his new clothes dirty, but Whitney reveals that he will need to change anyway and forces him into a jersey, much to Miguel's displeasure.

With Aipom, Politoed and Typhlosion, Miguel sets out to enter his first competition. Miguel picks the Skill Course, which ends with the round Snow Throw. Miguel's team throws snowballs at their opponents, but Miguel commands Aipom to create a gigantic one. Aipom throws it, giving Miguel enough points to win the Skill Course. Maximo hands Miguel the Skill Medal for being the winner. After meeting up with Whitney again, Miguel decides to pick the Jump Course next. Outside the dome, a large Pokémon swims through the lake with fury in its eyes.

Mary begins explaining how the Pokéathlon works over the speakers. She explains that there are five arenas where the Pokéathletes compete in each dome. Next, she explains that in the Sand Dome, the Disc Catch event is currently being held. Mary and Hirō decide to get a closer look and head inside to check on the competitors. Suddenly, Miguel rushes past Mary, accidentally causing her to spin around in the process. Once he realizes who he just passed, Miguel quickly moves back and re-introduces himself to Mary.

Mary and Hirō recognize Miguel as a troublemaker, which causes Miguel to be offended. Mary notices Miguel's jersey, which clues her into figuring out that he's competing. When Miguel is asked why he was running, Miguel reveals that he was making Aprijuice with the Apriblender. Mary questions Miguel's actions, as his Pokémon should be given orders while they are in a competition. Miguel reveals that he doesn't need to give his Pokémon orders.

In the Disc Catch competition, Sudowoodo and Vileplume easily catch a disc that was thrown to them. Miguel points out that most Pokémon would crowd together to catch a single disc, but since his Togepi is small, he can easily move through crowds. Togepi pushes his opponents away and easily catches the disc, which signifies the end of the match. The next round is Lamp Jump, where Miguel's team needs to push the lights while preventing their opponents from doing so. While Sudowoodo and Vileplume easily touch some lights, Togepi rudely pushes his opponents out of the way. Mary notes that Togepi's rude nature is just like Miguel, which she thinks makes them just like twins. Lamp Jump ends, which gives Miguel enough to points to earn the Jump Medal.

Later, Hirō asks Mary where Miguel headed off to. Mary states that Miguel had entered the Stamina Course and is entered in the Ring Drop competition with Typhlosion, Aipom, and Politoed. After Miguel wins the Stamina Course, Mary notes that Miguel doesn't pay attention to his team during competitions while she watches Miguel and his team laugh at Togepi's failed attempt to drink Aprijuice. Next, Miguel decides to enter in the Speed Course. This worries Hirō, who realizes that if Miguel plans to enter in the Speed Course, he will have to face Jet, a competitor that he may not be able to defeat.

In the Track Dome, Miguel is surprised to see so many people entering to watch the match. Miguel notices Jet next to him, who is blowing kisses to his many fans. In the Hurdle Dash and Pennant Capture competitions, Mary and Hirō's hunches are proven correct as Jet's team easily defeats Sudowoodo and Vileplume. In the final match, Relay Run, Miguel is behind Jet, which means he needs to win this match in order to win. The match starts, to which all the competitors and their Pokémon begin running.

Mary hosts the event and points out that some competitors will switch their Pokémon immediately while others may wait until their first Pokémon gets tired before changing. When she questions where Miguel is, they notice that Miguel is simply sliding on the ground slowly while riding on his skateboard in the wrong direction. An exhausted and in last place Sudowoodo struggles to move on, so he is switched for Vileplume. Mary points out that there isn't much time left on the clock, so Miguel switches Vileplume out for Togepi.

Togepi's fast speed allows it to easily catch up to Jet's Dodrio, but he is kicked away into the gravel by Dodrio's foot. The dirt gets into Togepi's eyes, preventing him from being able to see and run properly. Miguel commands Togepi to keep going and gives him directions on where to move. This causes Mary and Hirō to realize that Miguel wasn't playing on his skateboard, but was actually memorizing the field they were competing on. Togepi continues running and eventually manages to make it past Jet's Dodrio, which gives Miguel the win. Jet commends Miguel for his performance, which Miguel thanks him for. Mary goes up to congratulate Miguel for his win in the Speed Course. Mary points out her surprise to see how Miguel and Togepi understand each other perfectly. While he cleans Togepi's eyes out with a napkin, Miguel reveals that he has been with Togepi since he was an Egg.

While Miguel checks out a monitor, DJ Mary is approached by Magnus, the owner of the Pokéathlon. Magnus, with tears in his eyes, expresses delight to see a Pokéathlete like Miguel, and is glad that he opened the Pokéathlon in Johto. Whitney approaches Mary, who is surprised to see her friend competing. Whitney tells Mary that Miguel asked her to take him there, and she has to keep a close watch to keep Miguel out of trouble. Mary understands and goes back to her broadcasting duties. Whitney goes over to Miguel and asks what course he's planning on taking next. Miguel decides to take something similar to the Skill Course, as Aipom's strong tail will give him an advantage. A voice appears and points out that if an Aipom's tail gives it an advantage, then a Machamp's four arms will give it an even bigger one. Suddenly, a Machamp appears behind Aipom, and behind the Machamp, four figures.

The figures reveal themselves to be Bruno, Koga, Will and Karen of the Elite Four. Upon seeing the four, Miguel tries to say who they are, but has no idea who the people are, causing the Elite Four to fall down in frustration. Whitney attempts to tell Miguel who they are as well, but also has no idea who the Elite Four are. Embarrassed, the Elite Four introduce themselves and reveal that after talking to the Pokémon Association, they now work for them despite their dark pasts.

Will points out how it's funny they have to help wholesome Trainers. Karen reveals that they are there to help out at the Pokéathlon while promoting the Pokémon League. Miguel asks if that means that they are there to compete against others. Bruno offers a challenge in the next course, which Miguel proudly accepts. At the Power Course, Miguel is shocked to see his team being defeated by his opponents. At Circle Push, Koga's Muk easily pushes Typhlosion, Politoed, and Aipom away from it. In Goal Roll, Will's Exeggutor kicks several balls into a goal while Aipom, Typhlosion, and Politoed fail to block them. During the final round, DJ Mary points out how Miguel is losing despite his performance in the previous rounds.

In Block Smash, Miguel faces Bruno and his Machamp as his final opponent. Machamp does a powerful blow that destroys a whole row of blocks instantly. Whitney is shocked to see how powerful Machamp is as it destroys another set of blocks. On Miguel's side, Aipom attacks the cracked area in the center, but doesn't do much to the block. He switches to Politoed, but he only manages to destroy one. Miguel switches to Typhlosion next, who manages to break more blocks and is the closest to matching Machamp, but not by much. To Whitney's confusion, Miguel switches Typhlosion with Aipom.

Bruno confidently states that it's over, but Miguel begins laughing smugly. Bruno questions Miguel's motives, but he reveals that although he knew that he can't possibly beat Bruno with power, Miguel can win by getting critical hits on the blocks. By doing so, it sends Miguel's team into High Tension mode, allowing him to quickly catch up with Bruno. Bruno tries to fight back, but Machamp's arms have become too injured to be used again. Miguel has Aipom leap into the air and send a powerful strike in the dead center of the block, destroying them all and giving Miguel the win. Everyone praises Miguel for his win, but Bruno reveals that he knows that Miguel is actually hiding something from them. When Miguel asks how Bruno could tell, Bruno states that he saw it in Miguel's eyes. With his cover blown, Miguel reveals that he came to meet with Lance to get information on Arceus. Bruno turns solemn as he recognizes the man's name, but Whitney angrily attacks Miguel, as he had asked her to escort him to the Pokéathlon to compete in it. A pained Miguel apologizes, explaining that he was ordered on a secret mission by none other than Professor Oak, so he couldn't tell her.

In a flashback, Miguel explains that Professor Oak had suddenly called for him and showed him photographs of Team Rocket members lurking in various places: the Bell Tower, the Lake of Rage, and Goldenrod Radio Tower. Professor Elm confirms that Oak was concerned that Team Rocket was working towards yet another revival, and cooperated with the Violet City police in an investigation, where they received a message from Lance in the form of a 3-D holographic projector. In his message, Lance revealed that Team Rocket's objective was none other than the Mythical Pokémon, Arceus, and therefore requested that Oak send a Pokédex holder to him for more information. However, Miguel remained disinterested, and asked if Martinez or Rosita couldn't go instead. Oak reveals that Rosita is away doing research and that he isn't able to contact Martinez, prompting Miguel to fly into a rage as he realizes that he was asked because there was no other option.

Miguel rounds off his explanation by bragging that Oak practically had to beg him to take the mission, but Whitney and the others note that he's merely a substitute. Will and Karen note that Miguel should be meeting with Lance soon, but Koga catches wind of something huge approaching. A massive Dragonite from the sea which embarks on a rampage, destroying everything in sight. Hirō quickly declares a state of emergency and has everyone evacuate the stadium, while Bruno and Koga send out Hitmonlee and Ekans to fight, but both Pokémon are defeated by a single Hyper Beam attack. The Dragonite charges at announcer's podium, destroying it and leaving Hirō hanging onto the raging Dragonite for dear life. Spontaneously, Miguel changes back to his normal clothes and sends out Aipom, Politoed, and Typhlosion.

Calling to Koga and Bruno, Miguel reveals that he's asked Aipom to get Dragonite to attack him, and asks the men to signal him when Dragonite's Hyper Beam is about to fire. At the signal, Miguel launches Togepi's Poké Ball with his billiard cue, which meets the devastating attack. Miguel is sent flying and the Poké Ball is left smoking after being struck at close range. The Elite Four note that Miguel must have aimed for releasing Togepi before Hyper Beam hit, but the tactic was too risky and clearly failed. Pushing himself up, Miguel states that his tactics never fail, and sure enough, Togepi attacks Dragonite from behind, slamming a Double-Edge at the back of Dragonite's head and defeating it.

Everyone else is surprised that Togepi actually succeeded, and Whitney wonders if Togepi had escaped the Hyper Beam earlier. Karen disagrees, realizing that Togepi must have taken the Hyper Beam head-on, pushing through the attack with sheer determination. Koga and Bruno note that both Pokémon and Trainer are incredibly reckless, to which Miguel insists that he thinks everything through, noting a torn piece of cloth in Dragonite's claws. Based on research, Miguel knew that Lance had the ability to redirect his Pokémon's Hyper Beam attacks, as he demonstrated years ago, but this Dragonite's Hyper Beams were all fired straight, suggesting that Lance isn't around to command it. Whitney notes that Dragonite is badly wounded, and Bruno guesses that Lance must have lost a battle somewhere leaving the anguished Dragonite to escape and go on its rampage.

Annoyed that he wasted a trip, Miguel decides to go home. Nudging Hirō, he asks for a lift back halfway and thanks the Elite Four for a good time. Bruno thanks Miguel, and hands him Dragonite's Poké Ball, having managed to return it since the Pokémon recognized him. Miguel offloads a bunch of specialty snacks on Bruno, and as the Elite Four wave goodbye to Miguel and Whitney, Bruno is amazed at how tasty the Rage Candy Bar is.

Riding alongside Miguel, Whitney is perturbed that Miguel isn't the least bit concerned about Lance or Team Rocket. Miguel casually dismisses her, saying that he feels that those issues should be left to the police, but he's mostly interested in seeing Arceus, as everyone seems to be discussing it. On a whim, he asks Hirō to head for Ecruteak City so he can see the Kimono Girls. A bemused Whitney remarks to herself that Miguel is quite the big moron as the Goldenrod Radio Tower van heads north.

In the morning, Miguel is at the Kimono Dance Theater at Ecruteak, marveling at the performance of the Kimono Girls. As the traditional dancers respond lightheartedly to Miguel's compliment, Hirō shows up in front of Miguel, blocking his view of the dancers. Miguel knows exactly what Hirō's trying to tell him, and retorts by telling him to look at his Pokémon first. Miguel slides open the theater's back door to show Hirō that his Pokémon are training by themselves. Miguel explains that Aipom is learning a new move after being impressed by his teammates's battle against Lance's Dragonite. Miguel then knows exactly why Hirō is waiting for him to finish, rather than return to Goldenrod City. Miguel claims that Hirō wants exclusive coverage of what is about to take place, and also guesses correctly that Hirō had been spying on him and Edge at Mt. Silver when they were training. At that moment, Aipom successfully hits both Politoed and Sudowoodo with Double Hit, and evolves into an Ambipom as a result. The Kimono Girls also witness Aipom's evolution with marvel.

Togepi, however, kicks a stone, and the Kimono Girls can tell that it seems frustrated that it can't evolve. Miguel admits that Togepi still hasn't opened up to him yet, and someone walks in to echo Miguel's thoughts that the criteria for his Togepi to evolve are still very much elusive. Miguel sees a man with his Gastly and Misdreavus, and asks for his name. The Kimono Girls reply that he is Morty, the city's very own Gym Leader. Hearing Morty's name makes him remember that he was also at the Indigo Plateau exhibition matches sitting next to a pretty lady. Morty, knowing that Miguel is referring to Jasmine, states that she has moved to the Sinnoh region to take part in Pokémon Contests. This causes Miguel to sulk and think about leaving.

Kuni, the Kimono Girl who owns a Vaporeon, then asks Morty the reason for his visit. Morty states that he is simply on patrol, but knows that requests for his clairvoyant vision have spiked recently, making him wonder if anything has happened at Ecruteak. While the Kimono Girls also don't spot any signs of danger, Miguel is suddenly intrigued at Morty's claim of clairvoyance. After hearing Kuni's explanation of Morty's skill, Miguel immediately tugs at the man begging for his assistance in finding someone called Lance.

While ignoring Hirō, Miguel searches his pockets for the torn piece of Lance's cape, but his Pokédex falls out in the process. Thinking that Miguel was the person he was arranged to meet up with, Morty beckons Miguel to his Gym. Inside, Morty confirms Miguel's request, but just as he is about to proceed with his clairvoyance, the Gym telephone rings. Morty learns that Falkner, Bugsy and Chuck have stationed themselves outside, and thanks them. Morty explains to Miguel that the sudden interest in his abilities meant that the Ecruteak Gym was broken into a few times, which was why he hired his Gym Leader colleagues to add further steel to his compound.

Morty surprises Miguel by saying that he once used his clairvoyance to locate none other than Miguel himself, and then witnessed his heroic actions at the Indigo Plateau. Miguel responds by saying Morty knows more about him than vice versa. Finally, Morty begins to use his clairvoyance. Because it was difficult for Morty to describe his thoughts in words, he decided to sketch them instead. Suddenly, Martinez shows up at the door, so Morty asks him who he is. Martinez shows Morty his Pokédex, and is allowed to proceed. Finally, Miguel and Martinez both meet each other again, each with the intent of hearing Morty's thoughts for the future. Morty stands by, apologizing to Martinez for thinking Miguel was him. Martinez wraps his arm around Martinez's shoulder and says he doesn't know why Martinez's here, but can explain how he knows the boy. Miguel doesn't get to explain, as Martinez points out that he can feel a rumbling beneath them. Morty calls Chuck from the Gym phone. Outside, Chuck, Falkner, and Bugsy all stare in shock as Arceus appears before them. A blast of light sends Morty, Martinez, and Miguel flying, and as Martinez and Miguel question what the blast of light was, Togepi looks on with a frightened expression.

Once Miguel can see Arceus with his own eyes, he dubs Arceus a complete mystery to him, but knows nonetheless that the creature standing before him is Arceus. Still, Miguel says a Mythical Pokémon can't attack out of nowhere like that. He sends out Typhlosion to fight and orders him to use Blast Burn, but Arceus easily reflects it. Next, Miguel sends out Ambipom and orders him to use his new move, Double Hit. Ambipom, too, is easily defeated by Arceus. Miguel goes to ask Martinez what they should do, but Martinez is nowhere to be found. Miguel and Ambipom are then forced to dodge a blast from Arceus, and Miguel finds himself almost careening into the water until Typhlosion grabs him and pulls him back. As Typhlosion runs from Arceus with Miguel on his back, Miguel reflects on telling Lance that he wanted to see Arceus in person, but now regrets it. He also reflects on how Lance was supposed to give him information on Arceus, but it's too late now that Arceus is in front of him.

Miguel tells Typhlosion to stop running after he spots Bugsy lying on the ground, holding a bug catching net. After trying to wake Bugsy up to tell him to escape, Miguel resorts to asking Typhlosion if he can give Bugsy a ride. Arceus approaches and looks as if it's about to attack the trio, but flies away. Miguel asks Arceus why it has a sad look on its face and claims that he can help if Arceus wants him to.

Miguel asks if Bugsy is awake as they chase after Arceus on Typhlosion's back, though he first calls the Gym Leader a Bug Catcher. Bugsy is surprised to see Miguel and asks what happened. Miguel explains that Arceus destroyed the Ecruteak Gym, then laments that he doesn't have time to review the information Morty gave him. When Bugsy inquires as to what the information pertains to, Miguel says he wants to know the whereabouts of Lance. He shows Bugsy the drawing given to him by Morty, and Bugsy recognizes it as the Ruins of Alph, as he has researched the area for years. When Miguel asks Bugsy where the Ruins of Alph are, Bugsy notes that they're currently on Route 36 and encourages him to keep following Arceus. Miguel and Bugsy reach the Ruins of Alph, but see no sign of Lance. From its Poké Ball, Dragonite lunges out from Miguel's pocket and toward an entrance into the Ruins of Alph. Miguel follows with Togepi, and both are almost struck by Tyranitar. Miguel greets Lance, upset that Lance ditched him at the Pokéathlon, and Lance explains that he was ambushed by an attacker in disguise. Having confirmed Lance's identity, Miguel returns his Dragonite to him.

The two talk about the Pokétathlon. Miguel confirms he won all five medals, and Lance is impressed, but he's not sure the Pokédex holders can help Arceus because of how deep Arceus's hatred for humanity runs. As proof of this, Lance points out that Togepi isn't attached enough to Miguel to evolve. Miguel is about to demand an explanation, but Bugsy calls to him, saying Arceus is here. Though Lance believes it might be pointless, he hands Togepi a Shiny Stone just in case before Togepi follows his Trainer.

Outside, Miguel prepares to fight Arceus and releases Vileplume, Sudowoodo, Ambipom, and Politoed alongside Typhlosion and Togepi. Arceus retaliates by creating a barrier which traps Miguel and his Pokémon inside; Miguel pushes and slams into the barrier, but it doesn't budge. He orders Typhlosion to use Blast Burn, then introduces himself to Arceus and asks it why they have to fight if he's just trying to save it. All of his released Pokémon, however, are struck at once by an attack by Arceus, and Miguel wishes for them to stand their ground until Martinez arrives.

Elsewhere, Hirō arrives at the Ecruteak Gym with a Dusknoir at his side. Hirō vouches for them to follow Miguel, hoping to get a scoop.

Back to Miguel's fight with Arceus, he and his Pokémon continue to be hit with an attack Miguel doesn't recognize. Miguel asks Arceus directly what it wants him to do, and Arceus responds with another blast that sends Miguel and his team flying backward. He notes how Arceus looks sad and how he couldn't help but become determined to learn more about it from the time they first met. Since Arceus won't tell Miguel anything, Miguel consults his Pokédex.

Lance and Bugsy look on from inside the Ruins of Alph, where Bugsy points out Arceus's barrier before Lance begins the tale outlining the Pokéathlon's origins. The tale consists of an island plagued by illness and a Pokémon Trainer setting off to find a Mythical Pokémon that could give them the cure. Once the Trainer and his Pokémon became one, only then did the Mythical Pokémon tell them the cure. The Pokéathlon was created to celebrate this Trainer's achievement; the sports are meant to represent the obstacles the Trainer had to go through in order to find the cure. Lance then claims that he wanted to meet Miguel at the Pokéathlon Dome to see if Arceus's heart could be thawed by meeting a similar Trainer. When Lance finishes the story, Bugsy wonders exactly which species of Pokémon gave the Trainer the cure. Now healed, Dragonite is released from its Poké Ball and flies off with Lance, leaving Bugsy confused as to why Lance isn't staying to handle the situation with Miguel and Arceus.

Soon afterwards, Martinez and Rosita arrive on Martinez's Honchcrow, and as they enter the barrier to rescue Miguel, and with all 16 Plates in hand, everyone is transported to the Sinjoh Ruins, where there's cold and snow. Rosita, Miguel, and Martinez are by themselves, wondering where exactly they are. Miguel notes that Arceus had a strange look on its face once Rosita and Martinez descended into the barrier before being transported. Martinez speculates that the Plates either belong to Arceus, or are a part of it, and so, Miguel suggests they give the Plates back to Arceus so it can hopefully stop feeling sad. Approaching the entrance to the Sinjoh Ruins, they spot Archer with his hands behind his back, eyes closed, and a smug expression on his face. Rosita demands to know why he's there, but Archer just responds with a story about how Sinnoh and Johto were part of a mass migration that caused their cultures to seep into each other. He notes that the Sinjoh Ruins look similar to where Arceus was first awakened, but that they're all neither in Sinnoh nor Johto. It is then revealed that Arceus is being tied up.

Proton thanks Rosita, Miguel, and Martinez for opening up Arceus's heart enough that it opened the barrier to the Sinjoh Ruins. Ariana and Petrel thank them for collecting all 16 Plates for them as well. As Arceus is led in chains to be enshrined on the Mystri Stage, Miguel tells Martinez to give Team Rocket the Plates, much to Rosita's surprise. Miguel, Rosita, and Martinez accost Team Rocket as they work to force Arceus on the Mystri Stage in the Sinjoh Ruins so that they can enshrine it. Ariana, Proton, and Petrel tell them that they'll have to defeat the three of them if they want to interrupt Archer and the enshrining process. At the start of the battle, Ariana's Murkrow fights Rosita's Meganium, Petrel's Golbat fights Martinez's Weavile, and Proton's Zubat fights Miguel's Sudowoodo.

Meanwhile, Archer shows Arceus the 16 Plates and notes how badly Arceus must want the Plates back in its possession. However, according to Archer, Arceus has to show him its power as long as he holds the Plates, so Archer holds a Splash Plate up and demands it change type. Arceus's body glows brightly, and the fight between Team Rocket and the Pokédex holders pause as they wonder what the light means. Proton points out that Arceus's new body color, a deep azure, means it is now a Water-type. Arceus promptly summons a wave of water, which sweeps the Pokédex holders away. Archer holds up a Zap Plate, changing Arceus to an Electric-type, then a Stone Plate for Arceus to become a Rock-type, then a Meadow Plate for Arceus to become a Grass-type, and finally, then a Mind Plate for Arceus to become a Psychic-type. Speaking to Arceus, Archer claims that he's not sure why humans wanted to extract Arceus's powers from its body in the first place, an event that caused Arceus to stop wanting to live in harmony with humans. Archer further claims what a waste it would be for Arceus to just sleep for the rest of time when its powers could be used for so much more, and so, that is why Team Rocket searched for it.

Rosita demands to know why Miguel told Martinez to hand Team Rocket the Plates just then, but Miguel says he doesn't know why. Announcing the names of all 16 Plates, Archer then claims that they belong to people who want Arceus's power. After thanking the Pokédex holders once again for their part in this, Archer demands Arceus to start creating. Several Unown appear and gravitate around Arceus's body. Proton, in response to Miguel's confusion, explains that Arceus can't create something out of nothing, and Archer claims Arceus is in the middle of creating the Creation trio. Archer boasts about Team Rocket's control over the Creation Trio and mentions Team Rocket's boss, Giovanni, causing Martinez to react with surprise. Archer wishes for Giovanni to know, if he's still alive, that Team Rocket has succeeded in becoming the most powerful organization in the world. Falling to his hands and knees, he begs for Giovanni to return to Team Rocket. Petrel approaches Martinez from behind, and claims that only he of the Four Executives knows that their leader, Giovanni, is Martinez's father. He explains that when he was being punished at Team Rocket's hideout by Archer for losing the Plates, he made the excuse that Martinez would seek all the Plates and thus, he would steal them all at once when Martinez finished collecting the Plates. Apparently, Archer was totally convinced by this excuse and Petrel was freed. Pondering his next move after Archer left, Petrel slapped on the disguise of Martinez, which caught the attention of the imprisoned Carr, who claimed that the black-haired kid was Giovanni's son.

Petrel goes on and says that he is now totally sure that Giovanni and Martinez are related, having seen Martinez's facial expression upon hearing the name Giovanni. Petrel's Golbat then slaps its tongue on Martinez, causing him to go blind. The corrosive saliva also burns Martinez's mouth, and before Martinez can react, he finds that he cannot cry out. After glancing at Archer, Petrel claims that "pleaders" like Archer are weak and limbless, for they become fixated on one thing and ignore all the rest. With an arm around Martinez's neck, Petrel assures Martinez no further harm and hopes the boy can work alongside him. Martinez manages to prompt Petrel for an explanation, but after hearing it, he gets angry. Petrel remains unfazed, claiming that from the first moment he and Martinez met, he knew Martinez was destined for a future of great evil.

Martinez admits that he could not escape from such a fate after all, and calls out his Honchkrow, using it to fly towards the center of the Mystri Stage. Realizing the implication behind Martinez's act, Petrel calls out towards Ariana and Proton, falsely claiming that Martinez is thwarting them, and soon Martinez is ganged up on by a Raticate, Vileplume, and a group of Koffing.

Rosita tries to help Martinez, but Miguel stops her. Miguel claims that Silver isn't the one who suddenly gives up. At that moment, a Poké Ball drops in front of Rosita, who sees that it's that of Martinez's Feraligatr. Miguel knows that Martinez threw Feraligatr's Poké Ball to them when he dived into the Mystri Stage, and he clearly knows what Martinez has in mind. Realizing this as well, Rosita smiles, and takes out the Poké Ball of her Meganium while Miguel gets Typhlosion's Poké Ball out.

Soon, Miguel and Rosita have Typhlosion, Feraligatr, and Meganium lined up, and order Blast Burn, Hydro Cannon and Frenzy Plant from them respectively. The attacks disintegrate the incomplete forms of Dialga, Giratina and Palkia, respectively. To Archer's horror, the particles of energy creating Dialga, Palkia, and Giratina vanish. The room falls silent, and Arceus turns towards the Four Executives. With a flash of light, the Four Executives "vanish" and Arceus starts absorbing the Plates.

Rosita uses Parasect to restore Martinez's vision with its spores. Miguel grins at Arceus, standing tall like its deity status suggests, and asks how it feels to be complete. However, Rosita suddenly sees broken fragments materializing on the three corners of the Mystri Stage. In no time, Dialga, Palkia, and Giratina materialize fully in each corner. Archer's maniacal laugh is heard, and Miguel turns around to see that the Four Executives didn't vanish after all. Archer states that once the creation process begins, it cannot be stopped and that it only appeared to be stopped because Arceus was absorbing the Plates. He claims that the creation of Dialga, Palkia, and Giratina, the completion of Arceus's state, the possession of these Legendary Pokémon by Team Rocket, and thus, Giovanni, is all destiny.

Archer's behavior frightens the rest of the Executives. Petrel decides to make his escape, without letting anyone else know, and starts to disguise as someone. Just then, a loud bang is heard. Ariana and Proton turn around and see a man wearing a hat and a trench coat. Upon being asked for his identity, the man is surprised that Ariana and Proton have forgotten who he is, and takes off his hat. Ariana and Proton exclaim in shock that Giovanni has returned. Martinez's attention is turned towards Giovanni as well, but suddenly remembers what Petrel said, however all doubt is eliminated at the next moment when he sees Petrel, half-disguised as Giovanni, struggling to stand up in front of the real Giovanni. Petrel tries to comment on the Ursaring that ruthlessly brushed him aside, and Giovanni coldly states that Ursaring was raised by his son. Before Martinez can properly reunite with his father, two other figures start to emerge. The figure that is standing sees that the legends have been created after all, and the other figure, sitting in a wheelchair, admits that this was the reason why the three of them came. The figures materialize behind Giovanni and are revealed to be Lance and Pryce.

The three Trainers begin combating the Pokémon, and manage to hold them off for a little while. When Miguel questions how Pryce returned, the man reveals that the one who saved him from the crack in time was Celebi, who could see the destruction that Arceus would bring with the legendary Pokémon it created. After everyone else leaves to take their battle outside, Miguel remains in the Sinjoh Ruins to calm Arceus down. Miguel sends out his entire team to try and face Arceus, but they are quickly swatted away and defeated again. The only one left standing is Togepi, who Miguel refuses to let fight as he does not fully trust in his power. Despite this, Togepi refuses to listen to Miguel's commands and continues to hopelessly attack Arceus.

Seeing how determined Togepi is causes Miguel to remember how they are both treated as last resorts, which puts them in similar situations. Miguel decides to trust in Togepi, and sends him to attack Arceus. As a result of Miguel's newfound trust in him, Togepi evolves into Togetic. As Miguel marvels at its evolution, Miguel suddenly remembers the Shiny Stone given to him by Lance, and throws it to Togetic, who proceeds to evolve into Togekiss, and delivers a Sky Attack, which doesn't hurt Arceus, but calms it down enough to end its rage.

At the Ilex Forest, Ken, Al, and Harry discover a Pichu hiding behind a bush. This Pichu gestures towards the bushes and a spiky-eared Pichu appears. The trio is overwhelmed by the two Pichu's cuteness and agree not to regard them as intruders. As the trio continue patrolling, a group of Team Rocket Grunts, led by four female seniors, interrupt them. The four senior Grunts accuse Ken, Al, and Harry of acting outside the commands of the four Executives.

Celebi, who has been collecting herbs in the forest, is then spotted by the four senior Grunts. They claim that Ken, Al, and Harry want to catch Celebi and use it to rebel against the four Executives, but the trio deny this and say they are following the orders of the boss Giovanni. The four Grunts don't believe them and start attacking the trio with their group of Sentret and Furret. They then decide to capture Celebi for themselves. After Al's Hypno uses Switcheroo to retrieve a piece of herb that one of the Furret stole from Celebi, Al urges Celebi to get to the Ruins of Alph immediately. Enraged, the four senior Grunts storm towards the trio, unaware that the two Pichu are in the way. Upon being trampled on by the four senior Grunts, the two Pichu immediately zap the Grunts and their Pokémon.

Meanwhile, the day is dawning at the Ruins of Alph. Dialga, Palkia, and Giratina appear from a portal on the ground. After being stared at by Dialga and Palkia, Giratina leaves through its own portal. Dialga and Palkia then fly away. Miguel, Martinez, and Rosita have by then also reappeared at the Ruins of Alph with Lance, Pryce, and the weakened Giovanni. Pryce recites the myth about Arceus, and everyone looks up to Arceus as it towers over them. Miguel then notices something familiar among the rubble. He initially thinks it's Bugsy, but in fact it's Petrel in disguise. Lance's Dragonite lifts Petrel off the ground with its tail. Lance is not impressed at the way Petrel abandons his comrades. Miguel recalls the fact that Lance was defeated by Petrel and wonders how it happened. Lance replies that Petrel had disguised himself as a girl with the same powers as him. Meanwhile, Giovanni continues to be tormented by his illness and admits that he would one day deserve what he gets for all his wrongdoing.

Suddenly, a voice calls out to Giovanni, and he sees Ken, Al, and Harry arriving with Celebi and two Pichu. The four senior Team Rocket Grunts, still on the trio's tail, are stunned speechless at the sight of Giovanni who had indeed returned as claimed. Miguel recognizes one of the two Pichu as his Pichu, and speculates the spiky-eared Pichu to be Pichu's girlfriend. Celebi gives its cure for the ailment to Giovanni, and miraculously Giovanni is able to stand up straight again. All the other Team Rocket members rejoice, and Giovanni states that Team Rocket is resurrected once more. Martinez is stunned by the turn of events, and is even more so when his own father asks if he would like to join. Martinez quickly gathers himself and turns down the offer. He states that he will bring down Team Rocket with his own hands someday. Giovanni is pleased at what he hears and welcomes his son's challenge anytime. With that, he turns to leave and is followed out of the Ruins of Alph by every member of Team Rocket.

Rosita is concerned that Martinez is letting his father go like that, but Miguel says that she should just let them decide what they want to do. Miguel then remembers what he wanted to say back then about Rosita's new outfit, but Rosita kicks him in the face before he can even start. Pryce then announces that he will be returning to his Gym.

Arceus begins to take off towards the skies. Miguel, watching Arceus take off, realizes that its rampage was not because of any kind of agenda, but to alert him to the fact that he didn't open up towards Togepi, and Miguel is glad that Arceus witnessed Togepi's evolution into Togekiss. With his mission finally over, Miguel decides to take a tour of Johto, and Togekiss offers him a ride on its back, with Miguel noticing that Togekiss's personality had changed completely. Miguel tells Crystal that he just wants to see Arceus off, and will return afterwards. With that, Togekiss takes off.