Edge/Crisis of Deoxys

Two years have passed since the Masked Man's defeat, and both the Kanto and Johto regions have been peaceful ever since then. In Pallet Town, a group of children try and capture a wild Nidorino. One boy throws a Poké Ball at the Nidorino, but it easily knocks the ball away. When the boy groans in frustration, another person approaches him and tells the boy that he should use the Gengar he has to battle it. The boy complies with the person and sends out his Gengar to battle the Nidorino and succeeds in facing it. The person who helped the boy is revealed to be Edge, who had returned to Pallet Town with Robyn Oak.

As Edge and Robyn walk to Professor Oak's Laboratory, they comment about how Pallet Town hasn't changed since they were last there. Upon entering the lab, Edge and Robyn notice that it is empty. They notice three devices with letters, that are addressed to Edge, Robyn and Roberta, placed next to them. Upon checking the letters, they notice that the text on them mentions Vermilion City.

Before they can open the letters, Edge and Robyn hear a commotion outside. They check what's happening, only to find an invisible opponent is attacking their Pokémon. They try and find out what's attacking them, but the enemy is too fast for the Pokédex to scan. Edge and Robyn have their Pokémon attack the opponent, but it dodges the moves and flies off to escape.

Edge decides that if Professor Oak is not there to meet them, then there must be a reason why he is not at the lab. Edge prepares to go and find Professor Oak, but Robyn decides to check out the Fame Checker that was included with the letters. Upon activating the Fame Checker, a recording of Professor Oak plays. Much to Edge and Robyn's shock, the recording reveals that Professor Oak intends to take the Pokédex away from them. A distraught Edge states that no matter how many times he plays the Fame Checker, it only plays the same message. Robyn just simply goes inside Professor Oak's lab and puts his Pokédex inside of a capsule. Robyn gestures for Edge to do the same, and with some reluctance, Edge hands his Pokédex over. The capsule begins glowing and after a bright flash of light, the Pokédexes disappear. The two Trainers decide that even though they don't know why Professor Oak told them this, they trust his decisions. Edge sends out Aerodactyl as Robyn hops onto his Charizard so that they can head off to Vermilion City. Edge notices that the letter addressed to Roberta is still on the table. Edge commands Venusaur to pick it up with his vines and hand it over to his Trainer.

Edge and Robyn enter Vermilion City through the skies. After arriving at the port, they jump off of their Pokémon and land on the ground, surprising the Sailor. After noticing that they have Tri-Passes, the Sailor pushes Edge and Robyn onto the ship as it is about to depart. After pointing out how one passenger arrived too early while two more arrived late, the Sailor quickly realizes that Edge are also Pokédex holders. The ship's announcer calls out that the Seagallop ferry is leaving and will be going to One Island.

Edge and Robyn wait as they ride the boat to One Island. Edge wonders what kind of place it is, but Robyn states that he has no clue. Suddenly, Pikachu bursts out of his Poké Ball and runs off. He approaches someone and begins tugging on their pants leg. The person is revealed to be Bill, who is surprised to see a familiar face. Pikachu shocks Bill, confirming to him that it's Edge's Pikachu. Edge and Robyn arrive at the scene and are glad to meet up with Bill again. When Robyn asks where Carly is, Bill states that she's at home. Bill reveals that he is also going to One Island so that he can help his friend, Celio, with the Pokémon Transfer System. Just then, Bill gets a call from Celio, who reveals that he can't get a connection for the Transfer System. Bill tells Celio to wait until he arrives so that he can get a look at it. The announcer for the ship announces that they have arrived at their destination.

Elsewhere in the ship, Roberta fights against the same invisible Pokémon that had attacked them in Pallet Town, as she's hovering in the air, being strangled by the mysterious force, while a black hole is created by the invisible Pokémon. Roberta tries to call out to her parents and get them to stop, but they fall into the black hole. The black hole closes and the Pokémon releases its grip on Roberta. Roberta falls to the ground and screams out in horror while Edge and Robyn stand near her.

Horrified at what happened to her parents, Roberta staggers over the edge of the ship and faints, falling off in the process. To save her, Edge jumps off the ship, rescues Roberta, and lands on the ground safely. Robyn notices that the invisible Pokémon is still on the ship and sends out his Pinsir to combat it. Pinsir attacks the opponent with its pincers, but it disappears before it can deal a hit. On land, Edge tells Robyn that they have to take Roberta to the hospital. Bill notices that Roberta's diary had fallen on the ground and sees that she had planned to meet her parents today. As Edge, Robyn, and Bill go to a hospital, a silhouette watches them from afar.

A few hours later, Roberta has been taken to the Pokémon Network Center and rests on a hospital bed. Although her injured team is being healed, Roberta's mental injuries will take much longer to recover. Edge asks Bill if it's true that Roberta had come to meet her parents. Although guilty for reading her diary, Bill shows the book and answers Edge's question. Edge realizes that the two people who were sucked into the black hole were Roberta's parents.

When Edge tries to figure out what is going on, Robyn decides to get answers by reading Roberta's diary. As he reads, Robyn finds out that Roberta had already gone to Pallet Town and returned her Pokédex to Professor Oak. The book goes on to state that Roberta was also attacked by an opponent after returning her Pokédex. Robyn guesses that the attacks must not have been a coincidence and pulls out Robyn's broken Silph Scope to get more answers. Despite the damages the machine took, it is still able to use its replay function to show the battle.

By looking into the Silph Scope, they see the red humanoid Pokémon attacking Roberta's team. Bill screams in confusion as to what the Pokémon is and why it attacked Roberta. Edge states that even though he doesn't know the exact details, what he does know is that he and Robyn will fight the Pokémon and defeat it. Bill questions their motives, as he doesn't know anyone stronger than Edge or Robyn, and that if they were defeated by the Pokémon earlier, it will be hard to get stronger and beat it. Edge agrees, but he states that they won't be able to stand for what happened to Roberta.

Robyn wonders if there's a way for them to get stronger quickly, but a voice tells him that there is. The voice states that One Island is known as a place where destinies intertwine, and as such, it must be fate that they met there. The voice reveals itself to be an old woman who tells Edge and Robyn that they will inherit her Ultimate Moves. Confused, Edge, Robyn, and Bill turn around and ignore the woman's words. Angered at their indifference, the woman waves her staff and sends two rings in Edge and Robyn's direction. Edge and Robyn immediately send Venusaur and Charizard out, who knock the rings into the air with a vine and tail, respectively. The rings fly into the air, but land perfectly on Edge and Robyn's wrists and lock tightly.

Robyn tries to attack the old woman, but she blocks his punch with her staff. The old woman calms down and states she only did that because they were going to leave her behind. She sends out a Typhlosion and Meganium and has them fire attacks at Edge and Robyn. The Trainers and their Pokémon dodge the attacks, but see that the ship was greatly damaged. The Sailor enters the docks to prepare for the next trip, only to be shocked at the damage. Angered, he tells the old woman—now revealed to be named Ultima—that she is going to be sent back to her home on Two Island.

Hearing Ultima's name reminds Bill of a legend of a woman who was said to know several strong Pokémon moves. Pleased at the introduction, Ultima confirms Bill's suspicions by stating that she is the same person. Robyn gets annoyed and tells Ultima to take the bangle off of his arm and unchain him to Edge. Ultima refuses, so Robyn decides to just leave, only to find out that the bangle forces him and Edge to be unable to get more than 20 feet away from Ultima. Angered, Robyn tells Ultima to stop messing with them, but Edge stops him. Edge tells Ultima that he has his doubts, but he will trust Ultima and asks her to teach them the Ultimate Skills. Ultima tells Edge that she will teach them her techniques.

Later, the Seagallop Ferry sails to Two Island, but Robyn tries to get the bangle off of his arm while Ultima sleeps. Robyn questions Edge's choice, as he believes that Ultima is not to be trusted. Edge states that since Ultima is stronger than them, they'll be able to get strong quickly. Robyn remains skeptical, as he points out that possibility that Ultima may be the master of the Pokémon that attacked them earlier. The boat arrives at Two Island, so Ultima wakes up and takes Edge and Robyn with her. As they walk, Roberta's Ditto reveals itself to have transformed into the pattern on Edge's backpack.

After walking up a long set of stairs, Edge, Robyn, and Ultima arrive at a very long corridor. Ultima reveals that her house is at Cape Brink, which is at the end of the corridor. When Robyn asks if this is where they will learn the Ultimate Skills, Ultima states that before she will teach them, they will need to develop their leg stamina. They arrive at an area called the Path of Jumping, where she has the two Trainers send out Venusaur and Charizard. Ultima hands one of Venusaur's vines to Charizard and states that Edge, Robyn, and their Pokémon will have to run through a backwards-moving floor while jumping rope.

Ultima goes outside on her Dragonite and states that she will observe them as they progress. Robyn asks Ultima when they will have to stop running, to which Ultima reveals will be when they reach the next area. She goes on to state that with each corridor they reach, the training will finish and a new one will begin. Annoyed, Robyn mocks Edge for his decision, but Edge states that they should finish what they started. Eventually, they manage to finish, and come across the second corridor, the Path of Catching. On the Path of Catching, Edge and Robyn are forced to ride a Dodrio each and catch the falling Berries whilst running on an even faster moving floor. After succeeding on the second path, they arrive at the final trial, the Path of Battling. When Robyn asks who they will fight, Ultima reveals that Robyn's opponent is right next to him. Much to their shock, Ultima states that she intends on teaching a skill to only one of them.

Ultima sends them both to the Path of Battling and tells the Trainers that they will have a Double Battle and can switch out any of their Pokémon at any time. Edge and Robyn quickly notice the floor moving again, but point out that the floor on the Path of Skipping moved backward, while the one on the Path of Catching moved forward with twice the speed. Unlike the first two paths, the floors on each other's side move independently from the other. Ultima appears in the window and explains that if a Pokémon scores a hit, the floor will move forward, but if one takes a hit, then it will move backward. She tells them that whoever reaches the next section first will win and has them start the battle.

Edge and Robyn start their battle by sending out two Pokémon each; Gyarados and Snorlax for Edge, and Magneton and Golduck for Robyn. Robyn and Edge express that neither expected to be battling each other here. Robyn points out that neither of them really have to go all out, as he doesn't really care who learns the Ultimate Skill as long as it means the mysterious Pokémon will be defeated. Edge agrees with his point, but wonders if Robyn will be satisfied with a battle like that. Robyn responds by having Golduck use Iron Tail and Magneton use Tri Attack on Edge's Pokémon. Robyn states that while he can take the easy way out, if his opponent is Edge, he doesn't have a choice but to go all out.

Edge has Gyarados use Hurricane on Magneton, while having Snorlax attack Golduck with Strength. Despite the damage he just delt to Robyn's Pokémon, Edge's floor begins to move backwards. Ultima points out that while Gyarados's Intimidate Ability did lower the damage of Robyn's team's attacks, his attack was still more powerful. Finally figuring out how the floor's movement works, Edge has Gyarados use Hyper Beam on Golduck. Robyn has Golduck take cover by going underground with Dig. Edge counters by having Snorlax use Earthquake, dealing damage to Magneton, twice the damage to Golduck due to it being underground, and having Gyarados unaffected due to him being part Flying-type.

The attack does enough damage to faint Robyn's Golduck, causing Robyn's floor to start moving backwards. Edge praises his team, but notices that Gyarados had been paralyzed by the effects of Tri Attack. Robyn states that their battle is a reenactment of their Pokémon League battle and expresses his excitement. Suddenly, Pinsir looms over Edge's head as he carries Machamp in his pincers. Pinsir drops Machamp, who proceeds to grab Snorlax's body. Robyn commands Machamp to use Seismic Toss, so the Superpower Pokémon rolls around and tosses Snorlax onto the ground. Edge points out that Snorlax is in trouble against Machamp once again and states that the combination with Pinsir increased the damage. Robyn commands Machamp to finish Snorlax off. Machamp rushes in front of Snorlax and moves to the side to perform a Low Kick, tripping Snorlax and sending him crashing into the ground, knocking him out. Edge comments that the attack was very effective due to Snorlax's large weight.

Outside the building, Ultima rides on her Dragonite. She comments about how Robyn knows how to make full use of his Pokémon during battles. Robyn follows by having Pinsir use Double Team, confusing Gyarados, before following with X-Scissor, knocking him out too. Edge sends out Pikachu and Aerodactyl as his last two Pokémon. Edge has Aerodactyl use Take Down, which doesn't do recoil damage due to his Rock Head Ability. Edge has Aerodactyl use Dragon Claw on Pinsir, so Robyn switches him out. Seeing an opening, Edge has Pikachu attack Machamp with Thunderbolt.

To Edge's surprise, the attack is suddenly redirected. Robyn smirks and reveals that he sent out his Rhydon, who has the Lightning Rod Ability, which causes all Electric-type moves to be redirected towards it. Robyn points out that they both only have two Pokémon left, but the winner will be decided by whoever reaches the end first. Robyn claims victory, but Edge refuses to back down. Edge decides that if Pikachu's Electric attacks won't work, then a body attack will work instead. Pikachu jumps into the air and delivers an Iron Tail onto Machamp's head. Both Trainers then reach the end at the same time.

Exhausted, Edge and Robyn collapse and attempt to catch their breath. Robyn questions who got there first, but Edge assumes they arrived at the same time. Robyn calls out for Ultima to decide the winner, but gets no response. They go inside to find Ultima, only to see a large shadow looming from above. They look back to see Ultima being choked by the Pokémon that attacked Roberta earlier. Edge and Robyn send out Venusaur and Charizard, but the mystery Pokémon grabs them with its tentacles.

Edge and Robyn comment that their situation had to have happened while they were exhausted. The bangles on their arms begin glowing and strange characters appear on them. Ultima struggles to reveal that the attacks they learned were Frenzy Plant and Blast Burn. They quickly realize that Venusaur and Charizard are reacting, indicating that they have learned the moves Ultima was training them for. With no time to lose, Edge commands Venusaur to use Frenzy Plant while Robyn has Charizard use Blast Burn.

Meanwhile, a gang of Bikers arrive at Three Island. One of the members tells the leader that the island is also called "Kin Island", due to the "parent" island being connected to the smaller "child" island via the Bond Bridge. After hearing about the Berry Forest, the leader decides to steal all of the Berries inside and burn the place to the ground. Suddenly, a girl chasing a Dunsparce emerges from the grass. She runs in front of the gang, forcing them to stop right in front of her. The leader gets angry at the girl and begins threatening her with violence. Before he can continue, a red humanoid Pokémon jumps up from the grass and goes on rampage, destroying the Bikers's bikes and sending the villains flying.

Back at the Pokémon Network Center, Bill carries a bunch of tools with his Farfetch'd. He worries about Edge and Robyn's decision to go train with Ultima, but shrugs it off as he goes to fix the Storage System. Bill passes by Roberta's room, where she still sleeps after the incident from earlier. Bill flashes back to earlier, when Edge and Robyn left Roberta in his care. Before they leave, Bill asks Edge if he finds it strange that they found three Fame Checkers and envelopes addressed to Edge, Robyn and Roberta, despite the fact that Roberta already had a Tri-Pass and returned her Pokédex to Professor Oak. Bill wonders what message is on her Fame Checker and what is inside her envelope. Edge agrees with Bill's thoughts, but decides that since they're there for Roberta, it should be her who inspects them. In the present, Celio tells Bill that they're done and he should go to the Network Machine. They notice that the system is being affected by an energy field, but aren't sure how it happened.

Back at Three Island, the Pokémon holds the Biker gang's leader up by his neck. After glaring at the Biker, the Pokémon tosses him aside and flies off. The terrified Biker notices another person has arrived and begs them for help. The person simply smacks the Biker away, angering him into thinking that the person must be allied with the monster that attacked him. In retaliation, he sends out his Magmar to attack, but the other person has his Nidoking attack with Rock Tomb. The mysterious person tells the Biker that he will have to try harder if he wants to be a bad guy. The man is revealed to be Giovanni, who corrects the Biker by stating that the monster is actually a Pokémon named Deoxys.

Back at Edge and Robyn's location, Venusaur and Charizard successfully unleash Frenzy Plant and Blast Burn, respectively, and the attacks fly towards Deoxys, but the force sends the two Pokémon tumbling backwards. Edge assumes that Deoxys dodged the moves and tells Robyn that they need to try again, but he notices that Venusaur and Charizard are too tired to use the attacks again. Robyn corrects Edge's assumption by stating that Deoxys didn't dodge, but their attacks missed. Robyn states that they made the mistake of using Frenzy Plant and Blast Burn without trying to calculate how strong the techniques would be.

Edge wonders if that means that he and Robyn are not skilled enough to master the attacks, but a voice tells him that he is wrong. The voice is revealed to be Ultima, who tells them that they will improve with enough practice. She tells Edge and Robyn that she is proud of them for learning her techniques. Confused, Robyn demands to know what Ultima is talking about and accuses Ultima for tricking them, but she states that she wasn't lying. Pointing to the Deoxys standing next to her, Robyn claims Ultima to be the mastermind of everything as she is allied with Deoxys.

Disappointed, Ultima takes back her praise for Edge and Robyn noticing the truth. Suddenly, Deoxys's head turns into Ditto. Ultima reveals that Roberta's Ditto had followed Edge by transforming into his bag. Ultima states that she and Ditto had become friends while Edge and Robyn were training and decided to have some fun with the two. Ultima repeats her intention to only teach her moves to only of them, but since Edge and Robyn were so equally matched, they were able to learn the moves before she could even teach it to them.

The bangles on Edge and Robyn's arm begin glowing and come off of their wrists. Ultima tells them that all they have left to do is perfect the accuracy of the moves. Ultima adds that when she was talking to Ditto earlier, it used Transform to show her exactly what happened to Green on the ship. Guessing that Deoxys is a powerful foe, Ultima hopes that her techniques will be used against it so she can hold her head up with pride. Ultima turns around and wishes Edge and Robyn luck. Feeling grateful, Edge pushes Robyn to the ground and thanks Ultima for her help.

Later, Edge and Robyn talk about their need to master Blast Burn and Frenzy Plant and rely on their instincts without their Pokédexes in order to face Deoxys. Edge talks to Ditto and wonders if it was so worried, that it had to follow them secretly. Robyn grabs Ditto and requests it to use transform into Deoxys again. When it does, Robyn points out that the form Ditto took was different than the one that attacked Roberta, implying that it can change its shape to suit the situation. Robyn states that if they don't figure it out, they won't be able to defeat their foe.

Edge gets a call on his Pokégear from Bill, who tells them to head to Four Island with the Rainbow Passes he sent to them. When Robyn demands answers, Bill reveals that Deoxys had appeared on the island. Bill states that the Tri-Passes won't get them to Four Island, but the Rainbow Pass will. Edge and Robyn go to the Icefall Cave, where Bill told them to rendezvous at. They comment that all of the Ice-type Pokémon makes the area completely cold. They notice two devices on a small rock and pick them up. The device releases a light, which points to an Exeggutor. Robyn assumes that it's attacking them, and commands Charizard to attack it with Blast Burn. Bill jumps into the scene and begs them to stop.

Bill apologizes for the mistake, and reveals that he was only trying to test out his invention, the Vs. Seeker. Bill explains that the Vs. Seeker is decided to respond to hostility and will shoot a beam of light to indicate any possible attackers. Edge assumes that the device will help them fight Deoxys, but Bill tells them that it only works on Trainers. Robyn gets annoyed and tosses the Vs. Seeker away. Bill states that he knew Robyn would say that, but reveals that it's the very reason why he called them there.

Bill reveals that a girl named Lostelle saw Deoxys at Three Island, and witnessed it defeated a bunch of Bikers, but didn't know if it did that to save her from them. He goes on to say that Lostelle mentioned that a man was there as well, and faxed a picture she drew of him. Bill presents the picture, which is revealed to be the Team Rocket leader, Giovanni. Bill expresses his confusion, as he thought that Team Rocket had disbanded. He wonders if Deoxys belongs to Giovanni or if it is simply a wild Pokémon. Edge decides that if Team Rocket is back, then they'll have to fight them once again.

Bill reveals that the reason he made the Vs. Seeker is that if they can use it to find the members of Team Rocket, then they'll be able to find Deoxys. Edge comments that this time, they're the predators instead of the prey. They take the Vs. Seekers, which immediately send out a signal, and go to where the beam ends. Suddenly, a group of wild Pokémon jump the group, which they assume belong to Team Rocket. Edge attempts to send out Venusaur, but the wild Pokémon are frozen by an unknown attack. A voice approaches from behind, who wants to join Edge, Robyn, and Bill in fighting against Team Rocket. The voice is revealed to be Lorelei, who is angry to have her home attacked.

Edge and Robyn express surprise to see that Lorelei of the Elite Four has come to help them. Lorelei explains that since Four Island is her home, she wants to help defend it from the villains that attempt to mess it up. As she explains, the frozen wild Pokémon break free from their ice prison and attack, only to be blocked by Lorelei's Cloyster. Lorelei has her Cloyster attack the opponents with Spike Cannon, sending them flying. As Lorelei continues to fend off the attackers, Bill expresses shock at her strength.

Lorelei states that she overheard their conversation and asks if Team Rocket is truly in the cave. Edge, Robyn, and Bill don't give a response, which Lorelei states she expected from them anyway. Suddenly, a voice over a speaker confirms Lorelei's question. Edge sends out Venusaur to defend, but a tank-like machine busts through the wall. On top of the machine sits a short, blond male with two Forretress at his side. The man jumps down as several clamps capture Edge, Lorelei, Robyn, Venusaur, and Charizard.

The man berates the wild Pokémon for not defeating their foes and knocks them away with his clamps while praising his Forretress. Edge and Robyn try to defend by having Venusaur and Charizard use Frenzy Plant and Blast Burn, but the attacks completely fail to hit their target. The man mocks them for missing, but a voice over the radio tells him to stop fooling around. Much to the man's annoyance, two more Team Rocket members arrive: a tall, pale woman, and a large, imposing male. The three introduce themselves as Carr, Sird, and Orm, the **Three Beasts of Team Rocket** that serve their boss with utmost loyalty.

Hearing them talk about their boss, Giovanni, angers Edge, who demands answers about Deoxys and what happened to Roberta's parents. Carr taunts Edge, who has Venusaur lift the clamp far enough for both of them to slip through. Lorelei tries to stop Edge, but Carr has his Forretress explode to defend himself. Orm expresses disappointment to see the battle over so quickly, but Sird notices that Lorelei managed to send out her Slowking in time for them to escape the attack. Sird attempts to berate Carr for his mistake, but he points out that even though they escaped, they can't hide from them.

Elsewhere, Lorelei, Bill, Robyn, Edge, and their Pokémon land in a house filled with stuffed toys. Robyn questions how anyone could live in such a place, but Lorelei points out that it's her house. Lorelei states that since they aren't far from the Icefall Cave, they have to stay hidden for a while. Suddenly, the Three Beasts appear on the television. They tell the people of the Sevii Islands to hand Edge, Robyn and Roberta over to them or else they'll begin destroying all of the Sevii Islands.

Robyn hears a rumbling sound and looks outside to investigate. An explosion shoots up from the Icefall Cave, and the Three Beasts emerge from it. Carr reveals that he will attack Five Island, Orm will attack Six Island, and Sird will attack Seven Island. Carr tells the people that if they want them to stop, they will have to hand over Edge, Robyn and Roberta.

Bill questions why Team Rocket would go to great lengths to just lure them out, but Robyn says that he doesn't care and is going to face them. Edge awakens and states that he will face them as well. Robyn questions Edge's health, as he was injured from Carr's Forretress's Explosion earlier. Edge states that he's alright, since they have to face three opponents with three people. Lorelei tells Edge to go to Five Island, Robyn to Six Island, while she will go to Seven Island. On the Seagallop, the Sailor mutters to himself about how everyone is treating the ship as if it's a cab. Robyn gets angry at this comment, scaring the Sailor.

Upon approaching Five Island, Edge sends out Aerodactyl and flies off. On Five Island, Carr begins attacking the area with his Steelix. Steelix's Dragon Breath begins destroying places such as Resort Gorgeous and the Memorial Pillar. Carr gets bored of an aerial attack and sends his Forretress to use Explosion at a Pokémon Center. The move fails, so Carr goes down to investigate. The culprit is revealed to be Edge, who mocks Carr for using Explosion again.

Angered by Edge's cocky attitude, Carr sends his Steelix to swallow Edge entirely. Edge is caught inside its mouth, but he gets out with Azumarill's strength. Azumarill uses Focus Punch on Steelix, sending it flying. Carr tries to counter with Steelix's Iron Tail, but Azumarill simply catches it in her hands. Azumarill lifts Steelix into the air by its tail and smashes it into the ground. As Carr questions how she did that, Pikachu threatens him with his tail.

Edge demands to know why Team Rocket is after them and assumes that they're doing it because they believe that he and his friends will disrupt their plans. Carr reveals that they aren't a hindrance to their plan, but is actually the key to its success. Carr reveals that Team Rocket's plan is use the Pokédex holders to lure out the DNA Pokémon, Deoxys. Edge realizes that Deoxys is the Pokémon who attacked Roberta on the Seagallop. Carr goes on to explain that Deoxys is attracted to Pallet Town's Pokédex holders.

Edge interrogates Carr about Deoxys. Edge notices a woman in pain and goes over to help her and has Venusaur hold Carr in place. The woman refuses Edge's help and claims that it was his fault that Team Rocket attacked the Sevii Islands. Bill appears and praises Edge for his victory over Carr, but Edge just looks depressed. When Bill asks what's wrong, the townspeople begin throwing rocks at Edge and tell him to leave. Bill defends Edge by stating that he fought for the townspeople as well as the fact that he's one of the Pokédex holders trusted by Professor Oak. The townspeople tell Edge to prove it by showing his Pokédex, but he states that he doesn't have it at the moment. Bill gets angry at the townspeople's claim that Edge is a liar, but Edge tells him that it's alright.

Suddenly, a pain begins affecting Edge's chest while a noise begins howling through the town. As he clenches his chest, Edge recites Carr's claim that the Pallet Town Pokédex holders are the bait to lure out Deoxys. When Bill asks what he is talking about, Edge states that although he doesn't know why, he can feel that Deoxys is coming. Suddenly, from a swirl of smoke, Deoxys appears in front of Edge. Carr expresses joy to see that Deoxys has finally arrived. Edge notes that although it's currently transparent, Deoxys's current shape is the one that Ditto saw. Suddenly, Deoxys's forme changes into the one that was recorded on Roberta's Silph Scope.

Edge has Pikachu attack Deoxys with a Thunderbolt. Before the attack reaches it, Deoxys shifts into a new, bulkier forme and blocks the attack with its tentacle. Edge realizes that Robyn was right in guessing that Deoxys can change its shape. Carr reveals that Deoxys's ability is called **Forme Change**. As Deoxys changes back into its first forme, Edge sends out Aerodactyl and flies towards it.

Deoxys responds by trying to tie up Edge with its tentacles, while the other one turns into a fist. While Edge is distracted, Deoxys sends a powerful punch at Aerodactyl's face. When Edge and Pikachu are knocked to the ground, Deoxys pierces Aerodactyl's wings with its tentacles. Edge has Venusaur catch the falling Aerodactyl with one of his vines. Edge sends out Snorlax, who attacks Deoxys with a Mega Punch. Deoxys switches into its bulky forme, making the attack useless. With no way to get around the Forme Change, Edge wishes that he had his Pokédex.

Edge decides to come up with a strategy himself and sends out Gyarados to battle. Edge notes how the forme with tentacles has a higher attack, while the bulkier forme has a higher defense. Despite figuring this out, Edge states that he can't figure out what the transparent form is. Carr praises Edge's observation and reveals that the tentacled form is called the **Attack Forme**, while the bulky forme is called the **Defense Forme**. Carr pulls out a black-colored device which is suddenly filled with Deoxys's information. Bill notes that although the color is off, the device Carr is holding is a Pokédex. Bill demands to know where Carr got the Pokédex from, but Carr just runs away to get more information on Deoxys. Bill tries chasing after Carr and demands to know if they captured Professor Oak.

Edge notes that the sky is being filled with thunderclouds. With the clouds in the sky, Pikachu is able to fire off a Thunder at Deoxys's chest. The attack deals a lot of damage, which Edge attributes to being because of Pikachu hitting Deoxys's core. As the smoke clears, Deoxys appears fine, which Carr reveals is because it used Recover. Edge tries to have Pikachu use Thunder again, but Deoxys's Pressure Ability prevents the move from being used again. Suddenly, Deoxys creates a ball of energy which shoots up from its core. Carr reveals the move to be Psycho Boost. While Deoxys fires the attack at Edge, Carr closes his black Pokédex and states that his observation is complete. Suddenly, Azumarill, Venusaur, Pikachu, Snorlax, Gyarados, and Aerodactyl leap in front of Edge. They protect their Trainer from the blast, but are heavily damaged in the process.

At Seven Island, Lorelei battles against Sird. Lorelei briefly gets distracted from a light emanating from Five Island, giving Sird an opening to attack. Lorelei retaliates with her Jynx and Slowking, knocking Sird's Starmie and Persian away. Sird notes how powerful Lorelei is, but reveals that he has prepared a trap for her. A rumbling fills the area, which Sird reveals is because she solved the Tanoby Key puzzle. Several Pokémon fly out of the Tanoby Chambers, which is revealed to be a large group of Unown.

The Unown defeat Lorelei's Slowking, but she sends out her Cloyster and attacks the Unown with Spike Cannon. Lorelei manages to win, but Sird claims that she has already won their battle. Sird's Starmie's core appears on the stone they are battling on. Lorelei tries to have Cloyster defend, but Starmie fires a beam at Lorelei's back. As she falls down, defeated, Lorelei realizes that Starmie used Camouflage. Sird points out that since Cloyster is Lorelei's strongest Pokémon, she had to distract Lorelei with the Unown so she could get in an attack with her Starmie. Lorelei calls Sird despicable, but the Team Rocket member takes it as a compliment.

Sird begins calling Giovanni to ask him of his current situation. Giovanni thanks Sird for stalling, as he wouldn't have been able to polish the Ruby and Sapphire in time otherwise. Giovanni reveals that Carr has reported that in addition to its **Normal Forme**, Deoxys has the ability to turn into its **Attack Forme** and **Defense Forme**. Sird notes that just like he predicted, if they use the Ruby and Sapphire, they will be able to use Deoxys's remaining formes. While Sird asks if she can pick the stones up, Lorelei's Jynx begins releasing a mist over Sird's leg.

Meanwhile at Edge's location, Edge continues to feel depressed over his defeat against Deoxys, just as Robyn, Roberta, Ultima and the Sailor arrive, and informs them of his crushing loss. Sitting by a fire, Edge, Robyn, Roberta, Bill, Ultima, and the Sailor camp out for the night. The Sailor holds a radio the broadcasts a message stating the current status of Five, Six, and Seven Islands. After consulting with Bill, Robyn confirms that in addition to its first two formes, Deoxys has two more, making it a total of four. Bill goes on and states that when Edge was almost defeated, Sird showed up on Five Island.

In a flashback, seeing Sird causes Bill to realize that she defeated Lorelei, but Sird states that the battle wasn't even a warm-up. Sird berates Carr for not defeating Edge and states that they'll return to Seven Island after seeing Deoxys's last Forme. Sird tosses the two stones at Deoxys, which gives its half-transparent form full color. Sird dubs the stones the Ruby and Sapphire, which contain the climate of Hoenn. Sird uses the Ruby and Sapphire to turn Deoxys into its last Forme. Deoxys turns into a thin Forme that quickly flies past Red, knocking him over. Sird names this last transformation the **Speed Forme**, which maximizes Deoxys's speed. Afterward, Sird and Carr leave in pursuit of Deoxys.

Back in the present, the Sailor wonders how they can defeat their opponents. Robyn states that it's not the first time they have face an opponent as strong as Deoxys. Robyn suggests looking for Lorelei in the daytime and tells Edge that they should go to Seven Island in the daytime. When Edge doesn't give a response, Robyn asks him what's wrong. Edge gets angry at Robyn and claims that he only said those things because he never had to fight Deoxys. They get into a brief fight, but Edge states that he will understand if he fought Deoxys as well.

Robyn suggests that they will have a chance if they work together to fight Deoxys, but Edge states that they will still lose. Robyn asks why Edge became a coward. Edge states that he is a coward, which he assumes is why the Pokédex was taken from him. Edge notes how he had become so used to the Pokédex, he became dependent on it. He states that because of the Pokédex, he and the others had become famous, but was treated horribly when the people saw that he didn't have it. Edge claims that without the Pokédex, he is nothing, and that Professor Oak must think that he's no longer qualified to own one. When Edge runs off, Bill tries to stop him only for Robyn to tell Bill to let him go. Although Roberta ran after him, Robyn tells them that they have more important matters to discuss. Robyn reveals to everyone that Team Rocket has his grandfather, Professor Oak, in captivity.

Elsewhere on Five Island, Sird and Carr make their way to their base, the Rocket Warehouse. After entering the password, Sird begins looking for Deoxys on her computer. Elsewhere, an "!" and "?" Unown spot Deoxys landing on an island. Sird calls Giovanni and informs him that Deoxys has returned to Birth Island. After turning back into its Normal Forme, Deoxys becomes encased in a pyramid-shaped barrier, which Carr calls the **Delta Shield**. Carr notes that although Deoxys managed to win against Edge, it still took a powerful Thunder to its core, which means that it needs time to heal.

Since Deoxys has been heavily injured, Giovanni tells Carr and Sird to leave Deoxys be for now. Carr notices a photograph that has been left behind. The photograph shows a younger Giovanni with a young, black-haired child being held in his arms. In his head, Giovanni notes how he will finally be able to see his son again. He recalls rumors about a Team Rocket Boss who had a son that went missing for unknown reasons. Since Deoxys will have heightened powers when it awakens, Carr guesses that Giovanni wants to use it to find his lost son. Giovanni sends out his Pokémon and goes off to Birth Island.

Meanwhile, Edge keeps running off, only to trip on the beach. He begins apologizing to his team for losing to Deoxys. He apologizes to Pikachu, who he claims fought the hardest against Deoxys but still lost. He begins crying and begs his Pokémon to forgive him. Roberta suddenly appears riding on top of Jigglypuff. Edge assumes she's here to berate him for being a coward. Roberta reveals that Ultima told her about all that Edge did for her. Roberta thanks Edge for selflessly risking his own safety and well-being by facing off against an opponent as strong as Deoxys, all of her sake, as well as mentioning how he was the one who stood up and fought for her when she fainted, all whilst embracing him.

Edge states that despite all he promised, he failed to find her parents as well as getting his Pokémon serious help. Edge claims that he's no longer worthy of owning a Pokédex. When Roberta asks him where he's going, Edge states that he's going to leave the Sevii Islands, as that will mean the attacks will stop. Roberta asks if Edge thinks that Professor Oak took the Pokédex away because he had given up on him. When Edge states that he does, Roberta tells him that he's wrong. Roberta reveals that Professor Oak took the Pokédexes so that they can be upgraded into a National Pokédex mode.

Edge checks the message recorded on his Fame Checker which told him to give up the Pokédex. Roberta points out how Team Rocket made the mistake in not knowing that Professor Oak recorded the message that he had with Orm. Roberta tells Edge that she's aware that knowing the truth about the Pokédexes won't change his fear about Deoxys. Even though only Edge knows how terrifying Deoxys is, Roberta states that she will fight as well. Roberta brandishes one of Ultima's bangles, which suddenly pulls the woman towards them. Ultima wonders how Roberta was able to steal the bangle from her, which causes Roberta to give off a small chuckle, saying that it was her "specialty". When Edge asks Green if she intends on learning the Ultimate Water-type move, Hydro Cannon, she points out how he recommended her to Ultima. Ditto jumps out of Edge's backpack and joins its Trainer. Edge tries to stop Roberta, but she tells him that she isn't fighting for her own sake, but for her parents's sake.

On Birth Island, Giovanni lands in front of the injured Deoxys. Giovanni notes that since Deoxys was injured in the battle against Edge, it couldn't be a more perfect chance to capture it. He sends out an Aggron and claims that the power of outer space belongs to him, and commands a Brick Break. Deoxys manages to get out of the way with Teleport. Although he praises Deoxys's skills and notes how the Delta Shield will protect it from attacks while also healing it, Giovanni states he can read Deoxys like an open book. He sends out his Beedrill and has it use Agility to boost its speed up to its highest. Deoxys dodges Beedrill's attacks, but the Delta Shield begins turning red, signifying that Deoxys is becoming nervous.

Giovanni has his Aggron smash the Delta Shield with a Brick Break. He throws a Poké Ball at Deoxys, which sucks it inside and fully captures it. Giovanni picks up the Poké Ball and gloats that Deoxys is finally his. He notes how the Delta Shield is a combination of Light Screen and Reflect, so he wasn't sure that Brick Break would work so well against it. He thanks Edge for helping contribute to the data they managed to gather on Deoxys. He reveals that the Ruby and Sapphire, which was handed to Sird, will put Hoenn's climate all throughout Kanto, which will allow Deoxys to change formes repeatedly.

At the Rocket Warehouse, Sird expresses delight in seeing Giovanni's successful capture of Deoxys. She tells Carr that they need to start the next phase of their plan. Carr is too distracted from the picture he found, so Sird yells at him to get his attention. Carr snaps out of it and puts the picture in his pocket while he follows Sird.

At Five Island, Edge continues walking around. He notices Robyn and the Sailor discussing strategies, while Bill is trying to fix the Pokémon Center. He looks around more and sees Roberta training with Ultima to help Blastoise master Hydro Cannon. He notes how Robyn and Roberta are fighting for their families, while he doesn't have anyone to fight for. He asks Pikachu if he's too scared to fight because he has no motivation. Pikachu sees through Edge's excuse, which Edge notes is because they had been through so much together. Edge tells Pikachu that Roberta, Robyn, Bill, and his Pokémon are his family, and Edge flashes back to his childhood.

A young Edge wakes up in a bed and walks down some stairs, where he's greeted by a middle-aged lady who tells him to have breakfast. As Edge eats breakfast, he looks out the house's window and sees many kids around Pallet Town with their parents, and Edge becomes rather sad while watching it, as Edge mumbles to himself that he'd wished he had the same, and Edge reads the sign on the wall: Pallet Town Orphanage. Edge thinks to himself as he doesn't remember his parents's face as he never met them, and wonders what kind of people his parents were.

Back in the present, Edge tells Pikachu that before Deoxys arrived, he could tell that it was coming. He describes it as a sharp pain inside his heart which caused his body to shake. He notes that the feeling went away when Deoxys left and guesses the feeling he had is somehow connected to Deoxys's arrival. Pikachu gestures to Edge, which helps him realize the reason why he has to fight Deoxys: to rescue Professor Oak and Roberta's parents from Team Rocket. In addition to this, Edge wants to find out what the strange feeling he experienced was. He thanks Pikachu for helping him spill his hear out and sets off to go and find himself.

Edge decides to head to Seven Island and find Lorelei, but he hears a voice in his head stating that they have already found her. Suddenly, a large spoon with Lorelei sitting inside appears in front of Edge. As it tosses Lorelei on the ground, the voice states that it agrees with Edge's current state of mind, as it also once went to find itself. Seeing the spoon causes Edge to realize that the being in front of him is the Psychic-type Legendary Pokémon created by Team Rocket, Mewtwo.

Edge asks Mewtwo why it saved Lorelei. Mewtwo states that it found her after it passed by Seven Island. Before Edge can continue, he wonders why Mewtwo can understand him. Mewtwo doesn't answer him, and instead pulls out Edge's team to note how heavily injured they are. When Edge asks why it's here, Mewtwo states that it wants to fight by his side. Elsewhere, Ultima is shocked to see that Roberta has finally mastered Hydro Cannon. She notes how Roberta was able to do it without having to go through the Paths of Jumping, Catching, and Battling like Edge and Robyn did.

Robyn arrives and once he sees that Roberta has succeeded in mastering the move, he asks her to come help him with something. They go to the Seagallop and find the Sailor trying to get something out from under the ship. The Sailor reveals that the propeller is being jammed by a large group of Unown clustered all around it. The Sailor notes that he saw them flying around on the night when Ultima called him to pick her up. Robyn guesses that they must belong to Sird, since she used them to beat Lorelei, and that they must have followed them and were used to spy on them.

Robyn decides that the only way to get the Unown off is to use the Ultimate Moves. He asks Roberta how her skill with Hydro Cannon is, as his Charizard doesn't have Blast Burn's timing completely done yet. Although the Sailor doesn't want them to risk destroying the propeller, Robyn tells him that they won't. They have Blastoise and Charizard use Hydro Cannon and Blast Burn, but the attacks are not stabilized.

Suddenly, Edge appears and contributes to the attacks with Venusaur's Frenzy Plant. The three attacks combine into one giant move, which blasts the Unown away. Edge apologizes to everyone and states that he will fight with them after all. They accept, but wonder where Edge went and when he saved Lorelei. Edge reveals that it wasn't him who saved her, but Mewtwo. When Robyn and Roberta see Mewtwo, they scream in shock.

A few hours later, Edge, Robyn, Roberta, Mewtwo, Ultima, and the Sailor sail on the Seagallop to face off with Team Rocket. When Robyn questions why Mewtwo is with them, Edge explains that since his Pokémon are injured and can't be healed immediately, he needs a strong ally to help him. Robyn questions how Edge can tell what Mewtwo is thinking, but Edge states that he can hear its thoughts through telepathy. Mewtwo tells Edge to stop explaining, as he is the only person who can hear it.

Mewtwo reveals that he gained the ability to speak through telepathy after being captured by Blaine and then being released afterwards. Since Mewtwo distrusts humans, there are only two people he can talk to: Edge, the only person who caught it in a Poké Ball, and Bayley, the person who fought side by side with it. Robyn tells Edge to snap out of it and notes that his Vs. Seeker is reacting to something coming from Seven Island. They find the signal coming from Seven Island's Trainer Tower.

A swarm of Unown begin attacking, which causes everyone to guess that the tower must be Team Rocket's headquarters. Robyn suggests using Charizard to break through them, but Mewtwo states that it'll be a hassle. Mewtwo creates a barrier and begins flying through the Unown. To try and defend from this, the Unown begin spiraling and turn into a giant tornado. The tactic manages to prevent the ball from fling through, but Mewtwo counters by turning it into a tornado of Psywave energy. The tornado sucks the Unown inside, defeating them once its dispersed.

Robyn notes how Mewtwo is just as strong as the Ultimate Moves combined, but Mewtwo states that it is simply following the time limit of the tower. Once they land, Edge realizes that they are at the Trainer Tower, where Trainers attempt to battle their way to the top. Edge decides to start defeating their opponents, but Robyn and Roberta just look in shock. They are revealed to be looking at their kidnapped family members, who are injured while being held by shackles.

They immediately run after them, but Edge and Mewtwo notice that they are simply holograms. Several mechanical clamps shoot up from the tower's spheres and capture Edge, Robyn and Roberta. Mewtwo easily slices through the clamps with its spoon and moves everyone down with its powers. Edge gets angry that Team Rocket used Robyn and Roberta's family to trick them, but Mewtwo states that its their fault for falling for the enemies' trick.

Edge guesses that Team Rocket's plan is to try and split them up since they saw how powerful the Ultimate Moves were. Mewtwo uses its psychic powers to search for the kidnapped family members so they won't be tricked by more holograms. Mewtwo points to a room, where they find Professor Oak held inside. Robyn immediately sends out his entire team to rescue his grandfather. Robyn tries to have Pinsir cut off the shackles, but an invisible wall stops the attack. A voice tells Robyn that the system is immune to Pokémon attacks.

The voice is revealed to be R, the computer of the Trainer Tower. Edge is shocked to see that the tower is alive, while Robyn just calls it stupid, which insults R into attacking his team. Mewtwo tries breaking the wall, but R states that not even Mewtwo's attacks will be able break through it. R pulls out a bunch of weapons and uses it to attack the group, but Mewtwo blocks it with a barrier. When R states that they won't be able to rescue Professor Oak, Robyn attempts to prove it wrong.

R notices something quick has entered its network system. The thing is revealed to be Robyn's Magneton, who moves to R's nervous system at an incredible speed thanks to its Salac Berry. Magneton uses Zap Cannon, which fries R from the inside, defeating it. Robyn has Magneton release his grandfather from his shackles. Robyn has Magneton release Roberta's parents from their shackles. Mewtwo points to another room, which has Roberta's parents held inside, now freed from their shackles. Roberta has a tearful reunion with her parents, but it's interrupted by several silhouettes who appear in front of the group.

A large crowd of Deoxys surround Edge, Robyn and Roberta. The group wonders why there are so many of them, while Edge notes that they only look like Deoxys. The Deoxys begin attacking, so Roberta has Clefable and Jigglypuff protect her parents and Professor Oak. The three Trainers send out Venusaur, Charizard, and Blastoise out to battle the Deoxys.

Outside the Trainer Tower, Ultima attempts to fight off the Unown herd with her Dragonite. She states that she intended on following Edge, Robyn and Roberta to help them, but she can't make it to the tower. When the Sailor wonders how they even made it inside, Ultima tells him that she saw Mewtwo get them inside with her powerful vision. Ultima assumes that the arms that grabbed Edge, Robyn and Roberta were designed to separate them so that they would each face Carr, Orm, and Sird alone.

Lorelei, now awake, tells Ultima that she may actually be wrong. Lorelei reveals that after being defeated by Sird, she had her Jynx release a mist around Sird's leg that allows her to track where she is. She reveals that Sird isn't at the Trainer Tower at the moment. According to her tracer, Lorelei states that Sird is heading towards Six Island at a very fast speed. Elsewhere, Carr and Sird ride on an airship and arrive at Six Island. They find Orm there, still unconscious from his battle with Robyn. Carr uses his Steelix to pick Orm up from the ground and drops him onto the airship. Ultima notes that despite the Three Beasts not being at the tower, Edge, Robyn and Roberta's Vs. Seekers still reacted to a signal coming from it. They realize that there must be only one person there waiting for them.

Back inside the Trainer Tower, Edge, Robyn and Roberta have trouble with the Deoxys crowd. A voice appears, revealing that they are called the Deoxys Duplicates, duplicates that Deoxys created after he captured it. The voice is revealed to be Giovanni who proceeds to recite Team Rocket's acronym. Giovanni greets Edge, as well as Mewtwo, who he considers to be an unexpected guest. Mewtwo immediately attacks Giovanni, but he dodges the attack. Giovanni questions Mewtwo's actions, as he was the one who created it. Mewtwo uses its telepathy to communicate with Giovanni, who it claims is an exception to the rule of it only talking to people it trusts.

Claiming that he only created it to suit his evil deeds, Mewtwo tells Giovanni that it only talks to him so that it can express its rage. Mewtwo tells Giovanni that it won't let another Pokémon suffer under him and leaps in to attack. The attack is blocked by three Deoxys Duplicates, who force Mewtwo back. Edge asks Mewtwo what it means by letting another Pokémon suffer under Giovanni again. Mewtwo notes that its and Deoxys species names are extremely similar. Giovanni assumes that Mewtwo must see some of itself inside of Deoxys, but he reveals that Deoxys is actually a virus from outer space that was mutated into a Pokémon.

Giovanni claims that Mewtwo failed because it was given a will, but since Deoxys had its will taken from it, the power of outer space is under his control. This angers Mewtwo, who tells Giovanni that he will pay. Knowing how dangerous Mewtwo is, Giovanni summons a suit of armor that covers Mewtwo. Giovanni calls it the M2 Bind, which is designed to restrain Mewtwo.

At Five Island, Bill exits the Pokémon Center. He expresses being restless due to being the only one left behind, but quickly snaps himself out of it. An injured Celio arrives after having escaped from the angry mob at One Island. He asks Bill to use his phone to call Lanette and Brigette.

Lanette answers the call. She states that he sounds weird, which Brigette explains is because she has him on speakerphone. Bill asks Lanette and Brigette to help them with the situation on the Sevii Islands.

Back at the Trainer Tower, the M2 Bind completely covers Mewtwo. The armor restrains Mewtwo, preventing it from moving. Edge tries to get the M2 Bind off with Venusaur's help, but Giovanni tells him that his efforts are useless. R comes back online and explains that the M2 Bind works like the restraints used on Professor Oak and Roberta's parents, but several times stronger. Robyn tries to have Magneton stop it again, but R stops it from moving with a virtual lock. Giovanni notes that although it is a smart computer, but since it was made by Carr, R has some crass programming.

Despite this, Giovanni claims victory as he now has Deoxys on his side with Mewtwo restrained. Giovanni sends the Deoxys Duplicates to attack the Pallet Town Pokédex holders. Confident that nothing can stop him, Giovanni leaves to go and continue his search for his son. Robyn tries to stop Giovanni, but is knocked to the ground. The Deoxys Duplicates attack, only to be blasted away.

The attacker is revealed to be Ultima, who blasted the Deoxys clones with her Dragonite. Seeing that Professor Oak and Roberta's parents have been rescued, she offers to get them away with her Dragonite's help. Roberta apologizes to her parents about having to leave them again, but promises to beat the villains. Ultima tells Lorelei to borrow her Dragonite while she stays behind to help. Roberta asks Lorelei to help protect her parents. Robyn tells his grandfather to go with Roberta's parents, but he states that he is staying for unfinished business. Professor Oak takes Roberta and reveals that intends on getting the Pokédexes that were stolen from him back.

At the Pokémon Transfer System Management Center, Lanette talks to Bill about the effect the Ruby and Sapphire had on Deoxys. Brigette notes that there are other Pokémon that have multiple appearances, like the 28 known forms of Unown and the spot patterns of Spinda. When Celio notes that they only look different, Brigette brings up Castform's four different transformations that change depending on the weather. Lanette suggests switching "weather" with "climate" to guess that Deoxys can change its Formes depending on where it is located.

With this information, Bill figures out that Deoxys can switch between its Attack and Defense Formes with Kanto's climate. Although he doesn't fully understand it, Bill guesses that the Ruby and Sapphire contain Hoenn's climate, which allows it to become the Speed and Normal Formes. Bill thanks the two for their help, but Brigette states that they still need to find out the stones's source of power. Bill states that she's right and that he'll call them later. As he runs off, Bill states that their help could be instrumental in stopping the plan once and for all.

Back inside the Trainer Tower, Deoxys's duplicates continue attacking. They determine from the clone's behavior that they're only puppets that the real Deoxys is controlling. Robyn suggests that they find the real Deoxys and attack it. Mewtwo apologizes for not being able help, as the M2 Bind only gets tighter when it tries to escape from it. Mewtwo tells Edge that the three of them will have to break the armor with their Pokémon attacks. Edge points out that R stated that the M2 Bind is immune to attacks, but Mewtwo suggests it is only because there is no attack strong enough to defeat it yet.

Much to Edge's confusion, Mewtwo suggests attacking the M2 Bind with Frenzy Plant, Blast Burn, and Hydro Cannon, as the attacks are super effective toward one another and will destroy the armor whilst canceling each other out and leaving Mewtwo unharmed. Although Mewtwo claims the tactic is risky, Edge decides to do it anyway. Edge reveals that the real Deoxys isn't there, since he doesn't feel the sensation that he usually feels whenever it's around.

On the Team Rocket airship, Giovanni is greeted by the Three Beasts. He asks Deoxys to uses its abilities. He hands it a handkerchief and asks if its original owner is still alive. Deoxys takes the handkerchief and uses its psychic powers to find out that the owner is in Viridian City. Giovanni has the airship chart a path to find his son in his hometown. Deoxys drops the handkerchief, which Carr quickly picks up. He asks Sird who Giovanni is looking for and asks her to tell him anything she knows. Since Sird doesn't answer, Carr reveals that the Giovanni is searching for the boy in the photograph—his son. Sird asks him what's wrong with capturing Deoxys so that they can find Giovanni's son.

Carr claims that they're searching for his son so that Giovanni can pick him as his successor. Since Giovanni had promised leadership to one of the Three Beasts, Carr claims that Giovanni was just using them to search for his son. Carr goes crazy and tries to attack the airship with his Forretress, but Deoxys attacks and knocks him out. Giovanni thanks Deoxys for its loyalty and tells Sird to dump Carr into the storage room. After tossing Carr away, Sird tells Orm to not get any ideas, but he states that he has no interest in power struggles and just wants to reunite Giovanni with his son.

Back in the Trainer Tower, Robyn decides to take the lead on the strategy they discussed since Edge can't sense the real Deoxys being there. Robyn asks Mewtwo to trust him and allow him to hear its thoughts. Mewtwo decides to allow Robyn to hear its thoughts with telepathy. R tells them that they should give up, as it is useless. Robyn has Edge trade Venusaur over to him in exchange for his Charizard.

Robyn explains that since Edge wasn't able to heal his team after the battle with Deoxys, Venusaur is currently the weakest of the three Pokémon needed in the strategy. Robyn states that he will use Venusaur's current strength as reference and have Charizard and Blastoise adjust theirs accordingly. Robyn calls to Roberta and asks her if she can make it up to have Blastoise use Hydro Cannon. She states that she can't, so Robyn tells her to aim from the floor and break through the ceiling.

Much to R's shock, Roberta has Blastoise break through the floor with Hydro Cannon. Robyn and Edge follow suit with Venusaur's Frenzy Plant and Charizard's Blast Burn. Robyn tells Edge to lower his power while asking Roberta to increase hers. Roberta has Blastoise increase his power, but it causes him to begin moving backwards from the force of the attack. Snubbull, Nidorina, and Jigglypuff try and hold Blastoise in place, but Professor Oak states that they aren't strong enough to handle it.

Roberta reveals that seeing the Pokédex again reminded of her skill as an **Evolver**. Snubbull immediately evolves into a Granbull, while Jigglypuff and Nidorina are given Moon Stones to evolve into Wigglytuff and Nidoqueen, respectively. With their new forms, the three Pokémon help Blastoise keep his footing. They focus the three Ultimate Moves upwards into the center. Robyn has Mewtwo jump into where the three attacks meet, causing a large explosion.

R laughs in victory and assumes that Mewtwo was killed, only to find broken bits of the M2 Bind on the ground. Mewtwo appears from outside the tower, with a spoon in its hand. Mewtwo slices through the Trainer Tower, cutting it in two and destroying R in the process. Edge notices that he and Mewtwo are the only ones outside of the tower. He wonders what happened to the others, but a blast of water shoots up a new Pokédex to him. Mewtwo and Edge fly off to face Giovanni in the final battle.

As he flies on Robyn's Charizard, Edge looks back at the Trainer Tower. Robyn looks back at Edge and tells him to go on ahead in his mind. Edge realizes that Robyn gave Charizard to him because Aerodactyl's wings are still pierced from the battle with Deoxys. Mewtwo confirms Edge's theory by informing him of what Robyn told it earlier. Edge puts his Pokédex in his pocket and tells Robyn and Venusaur that he won't let their efforts be in vain.

Inside the Team Rocket airship, Giovanni kneels on the floor in exhaustion. As he waits for his son, Giovanni notices Edge and Mewtwo quickly approaching. He commends their ability to get through R, the M2 Bind, and the Deoxys Duplicates. Noting that Edge wouldn't be defeated so easily, Giovanni decides to have a battle before he sees his son. Edge and Mewtwo quickly arrive at the airship, which Edge notes is changing shape. The airship opens up, revealing a battlefield. Edge's body begins quivering again, signaling that Deoxys is waiting for them. Suddenly, several poles shoot beams that become a pyramid-shaped barrier that prevents Edge and Mewtwo from escaping. After landing, Edge puts Charizard back in its Poké Ball. From the center of the battlefield comes Giovanni and Deoxys on an elevator.

Giovanni welcomes Edge and Mewtwo and asks them what it's like to be standing from their position. When Edge asks what he's talking about, Giovanni states that since Edge was the only one to beat him in battle, he stands on higher ground. Giovanni states that since he is a challenger, he will be facing Edge not as the Viridian Gym Leader or leader of Team Rocket, but a regular Trainer with no titles. Giovanni throws off his jacket and tells Edge to face him. Edge takes his jacket off in response, and Giovanni states that the battle will be a one-on-one between Mewtwo and Deoxys.

On the battlefield, Mewtwo introduces itself to Deoxys while the DNA Pokémon remains silent. Although it expresses annoyance at the Deoxys Duplicates it faced at the Trainer Tower, Mewtwo states that it's a pleasure to face it in battle. Immediately, Mewtwo attacks with its spoon, but Deoxys blocks the strike with its tentacles. Mewtwo continues attacking furiously, which causes the battle to quickly move into the air. Mewtwo tells Edge that he is free to give it any commands in the battle. Mewtwo rushes in to attack once more, but Deoxys rapidly shifts into its Speed, Defense, and Attack Formes.

Deoxys manages to knock Mewtwo onto the ground. Giovanni reveals that the Ruby and Sapphire's power has reached Viridian City, which allows it change Formes at a quick pace and change strategies in an instant. Mewtwo asks Edge for a strategy, but he states that he doesn't have one. Since any strategy will be countered by its Forme Change, Edge tells Mewtwo that it should attack with the strongest move in its arsenal. Mewtwo fires a blast from its hand and aims at the crystal in Deoxys's chest.

Edge tells Mewtwo to just attack the crystal in Deoxys's chest. Deoxys just blocks the attack with its arms. Giovanni expresses disappointment that Edge attacked without a plan. Giovanni has Deoxys attack Mewtwo with a barrage of punches. Mewtwo tries to counter-attack, but Deoxys blocks it with its Defense Forme and attacks with its Attack Forme. Giovanni notes that Edge specifically attacked Deoxys's chest and asks why he chose that strategy. Edge reveals that when Pikachu used Thunder on Deoxys's chest, it caused Deoxys to stop moving. Mewtwo rushes into an attack, but Deoxys rushes past it with its Speed Forme. As Deoxys grabs Mewtwo with its tentacles, Giovanni states that Edge correctly guessed that the crystal is Deoxys's core. Deoxys continues strangling Mewtwo, but a stray attack shoots down and pierces it through the chest.

Back on Seven Island, Ultima emerges from the rubble of the Trainer Tower. She gets annoyed that everyone forgot about her, but quickly starts falling off a cliff. Lorelei saves her with her Shellder's Icicle Spear, which pins Ultima to the wall. After confirming that Edge and Mewtwo have left while Robyn and Roberta are still inside, they decide to regroup with the others. After landing, Lorelei asks Ultima if she managed to get the item she was looking for. Ultima praises Lorelei's intuition and presents the item she was looking for: the Old Sea Map.

Back at the airship, Mewtwo successfully spears Deoxys in the chest with a spoon-shaped psychic energy attack. Deoxys quickly shifts between its Attack, Defense, and Speed Formes as it tries to clench its chest. Giovanni assumes that Edge's statement about not having a plan was nothing more than a trick. Mewtwo tells Giovanni that he's wrong, and that it simply followed Edge's instructions to hit Deoxys's core by any means possible. Mewtwo states that its style is trusting its master no matter the circumstances. Mewtwo claims victory, as Deoxys can't control itself. Edge notes that Pikachu is trying to remind him that when it hit Deoxys with Thunder, Deoxys used Recover to heal itself and attacked with Psycho Boost. Mewtwo decides to just attack again and prevent Deoxys from healing itself with Recover. Mewtwo reveals that its attack didn't just have the one blast and has several more blasts of energy shoot down from the sky.

Giovanni tells Deoxys to turn into its Defense Forme, but it is unable to change and simply takes the attack in its Normal Forme. With Deoxys too weak to change, Mewtwo brandishes its spoon and rushes in to attack. Edge tells it to be careful, but Mewtwo states that it has figured out Forme Change's weakness. Mewtwo continues attacking furiously, but Deoxys manages to barely block the attacks. Deoxys is knocked into a wall, so Mewtwo goes in for the finish. Just before it can strike, Mewtwo is pierced in the back by two tentacles. Mewtwo notices that the tentacles are from its Attack Forme, yet Deoxys is currently in its Normal Forme. Deoxys reveals that it was using an aurora to make it appear to be in its Normal Forme, when it was really in its Attack Forme the whole time. Giovanni notes that it was too close, but Deoxys has managed to use Recover in time. Giovanni states that Edge and Mewtwo are the strongest opponents he has ever faced, so he will let them witness the strongest move in Deoxys's arsenal: Psycho Boost.

Deoxys prepares a Psycho Boost and fires it. Mewtwo jumps in the way of the attack, damaging it and knocking Edge backwards. The attack sends Mewtwo flying towards a wall. Edge tries to send his team out to battle, but Mewtwo reminds him that it's a one-on-one battle. Mewtwo states that if they break the rule, the battle will be meaningless regardless of whether they win or not. Mewtwo states that it can still fight and manages to get back up. Mewtwo weakly throws a punch, which Deoxys retaliates by kneeing Mewtwo in the stomach. Deoxys continues attacking Mewtwo relentlessly. Giovanni tells Edge that he has no choice but to surrender. Edge states that although he knows that Deoxys is stronger because its team-uped with Giovanni, he cannot back down until he stops Giovanni and finds out why Deoxys causes the pain in his chest. Edge begins running towards Giovanni and claims that he will never surrender.

Edge manages to steal the airship's remote controller and uses it to fire a barrier around Mewtwo. Deoxys attempts to stop Edge by grabbing him, but the energy manages to surround Mewtwo in time. Edge tells Mewtwo to heal itself with Recover while he holds Deoxys off. When Giovanni realizes that Edge was aiming for the controller and not him, Edge points out that Giovanni once told him that a Trainer must use the battlefield to their advantage.

While Deoxys tries to take the controller away, Edge tells Mewtwo to use Recover before it succeeds. Mewtwo uses Recover, fully healing itself of the damage it took earlier. Deoxys attempts to use its aurora ability, but Edge tells Mewtwo that it's still in its Attack Forme. Giovanni tries to counter by having Deoxys take Edge into the sky with its Speed Forme. Since Deoxys is moving too fast, Giovanni notes that Mewtwo might hit Edge if it tries to attack. Edge states that it doesn't matter and tells Mewtwo to attack Deoxys's core even if he has to hit him.

Deoxys changes into its Defense Forme, but Mewtwo fires a powerful blast straight at its chest. The attack defeats Deoxys and causes it to fall onto the battlefield below. Giovanni questions why Deoxys turned into its Defense Forme when it could have easily blocked the move with its speed. Giovanni quickly notices that Deoxys is rapidly shifting between its Attack and Defense Formes. Giovanni realizes that Deoxys isn't in agony simply because of being hit by Mewtwo's attack, but because it can only shift between two Formes. Giovanni quickly realizes that this means that Hoenn's climate is no longer in Kanto, which can only be possible if someone had removed the Ruby and Sapphire from the amplification device they were placed in.

Meanwhile, at the Rocket Warehouse on Five Island, Bill and Celio have managed to remove the Ruby and Sapphire from the amplification device. Since without the stones, Deoxys's Forme Change will be crippled without Hoenn's climate.

Back inside the Team Rocket airship, Bayley notes how big the place is and gets lost. She goes through a door and finds Edge outside. She tries to explain what happened to Martinez, but can't say it properly. She is interrupted by Deoxys, who is calling out to her. She guesses that Deoxys is trying to tell them something because its time is up. Using her powers, Bayley tells Edge that Deoxys is claiming that it is him. Edge asks Deoxys to explain what it means by that. Giovanni tries to explain, but Sird steps in and tells him that he shouldn't over exert himself. Sird offers to explain everything herself and tells Orm to bring Giovanni back in the ship. Edge tries to stop Sird, but she and Orm send their Pokémon to surround Edge and Bayley.

While Orm takes Giovanni away, Sird begins telling the story of Deoxys's birth. Edge states that he already knows that Deoxys is a Pokémon from outer space that was mutated from a virus. Sird continues her story to when a rocket was fired into space by the Mossdeep Space Center. The rocket found and investigated the virus, which soon mutated into two life forms. They attached themselves to the Grand Meteor, where they fell to the Hoenn region and were found by Professor Cozmo. After a spy reported the findings to Team Rocket, they guessed that the life forms would become very powerful Pokémon.

When Hoenn was plagued by a catastrophe, the Mossdeep Space Center was attacked by Magma Admin Courtney. Although they were unsure of her motives, Sird used the opportunity to take the two life forms away. On the Team Rocket airship, they monitored the life forms and found out that they had powerful psychic powers that allowed them to find objects from far away. When she showed them to Giovanni, Sird pointed out that they could be used to find his son.

Sird tasked Ken, Harry and Al with taking the life forms to Kanto. Once the life forms were taken out of Hoenn, their appearances changed. They soon determined that depending on the area, the life forms could either change from their Normal and Speed Formes in Hoenn and the Attack and Defense Formes in Kanto. After learning more about the Formes, Sird came up with the idea to set up circumstances that would allow them both to switch between all four Formes at will. Later, Al reported that one of the life forms had escaped, much to Sird's annoyance at herself for trusting the three with the task.

Upon arriving at Kanto, Sird and Giovanni saw the destruction that the escaped life form had done. They soon found out that it went to Birth Island, where it set up camp. Giovanni assumes that the one called **Organism No. 2** went to Birth Island so it can complete its shape and awaken itself. He notes that Birth Island is the perfect place for Deoxys to do such a thing.

Back in the present, Sird states that they allowed Deoxys to roam free to make its psychic powers stronger, but at the cost of making it harder to recapture. To rectify this, they used **Organism No. 1** to attack Edge and his friends to provoke and anger him. When Edge asks what angering him has to do with anything, Sird states that Organism No. 2 reacts towards his anger. Remembering what Deoxys claimed earlier, Edge realizes that Organism No. 2 is only drawn towards him.

Sird confirms this and states that besides herself and Giovanni, the other Team Rocket members were simply told that their target was all three Pallet Town Pokédex holders, when it was really just Edge alone. She states that with the black Pokédex, they concocted a plan to capture Organism No. 2 after examining it during its battle with Edge. When Bayley asks what happened to Organism No. 1, Sird states that they "disposed of it", as it was no longer useful. In her mind, Bayley expresses disgust at the fact that Team Rocket sacrificed one to make the other stronger, but notes that Sird is withholding the real reason why Deoxys claims that it is Edge.

Sird claims that her story is finished and suggests that Bayley pry the remaining information from Organism No. 2 with her powers. She states that it's useless, as they have already reunited Giovanni with Martinez. Sird and Orm begin tearing up at the assumption that Martinez and Giovanni are having a family reunion. Suddenly, a large quake surges through the airship, which means that someone is piloting it. The airship tilts over, which knocks everyone off of it. Mewtwo manages to save itself, Edge and Bayley with its spoon while Edge grabs Organism No. 2 to prevent it from falling. Edge assumes that it's part of Team Rocket's schemes, but Mewtwo notes that Sird and Orm look surprised as well. Sird notes that the ship is on autopilot, which must mean that someone has hijacked the airship. The culprit is revealed to be Carr, who managed to get out of the storeroom with his hacking skills. Carr claims that he doesn't care if Edge was backed into a corner and Giovanni is reunited with his son, and that he will crush everyone on the ship into pieces, intending to become the next leader of Team Rocket.

Sird and Orm try to get to the cockpit and stop Carr, but Orm slips and falls off into the trees below. The force knocks the airship's controller from Edge's hands, which Sird takes with her Persian's Thief. Sird uses the controller to deactivate the airship's stadium mode and states that she has to get control of the airship before Carr crashes it. Now safe, Edge and Mewtwo head towards the cockpit. Edge takes Organism No. 2 with him, as he states that he can't leave it behind while it's injured. Edge attempts to shake the door open, but Carr states that nothing he will do will get it open. Sird appears before Carr on a video phone, but he states that nothing she can do will be able to stop him. Suddenly, Sird's Starmie appears, having used Camouflage to disguise itself as a wall. Starmie knocks Carr and the pilot's seat off of its position.

Sird tells Carr that she will not allow him to mess with Giovanni's reunion with his son. Carr praises Sird's tactics, but claims that he's better. A huge explosion rips a hole in the airship, sending Sird and one of Carr's Forretress's flying out of it. Carr reveals that he planted ten other Forretress on the ship and commanded them all to use Explosion so that if the ship lands safely, it will still be blown up. Carr escapes from the airship on his Skarmory and flies off.

Mewtwo breaks the door down and states that they have to get off the airship immediately. Edge states that they can't, as the Forretress could severely damage a town or city if they crash and then blow it up. In addition to that, Martinez and Giovanni are still on board as well. Edge asks Bayley to help him, but she begins dozing off from overusing her powers. Edge realizes that this was Sird's intention when she told Bayley to use her powers on Organism No. 2. Mewtwo states that although it agrees with him, it asks Edge what they should do. As it approaches Vermilion City, the airship tips over.

Edge states that he has a plan, but will need Organism No. 2's help. He has Organism No. 2 create a black hole to send Martinez and Giovanni somewhere else. Once they're safe, he sends Bayley and Mewtwo into it as well. Mewtwo tries to stop him, but Edge points out that the black hole is only an entrance to an exit. Mewtwo states that's not what it was talking about and asks what Edge is planning to do. Edge smiles and tells Bayley and Mewtwo that he will return safely as they continue to be engulfed. As Mewtwo sinks down into the black hole with Bayley, it asks Edge what he plans on doing. Suddenly, a fishing line shoots out from the black hole and surrounds Edge's hand. The culprit is revealed to be Bayley, who used her fishing pole to pull herself back up. Bayley states that if she leaves now, she won't be able to tell Edge the whole story of Organism No. 2. Since she will be falling asleep from overusing her powers, she'll have to tell Edge what she saw in Organism No. 2's mind.

Bayley reveals that Edge's blood flows inside Organism No. 2's body. Bayley states that in order to strengthen his forces, Giovanni collected various cell samples. One of the samples was the blood Edge left behind after their battle in Viridian five years ago. When Organism No. 2 escaped from Team Rocket's custody, it must have absorbed Edge's blood into its system after going on a rampage in Team Rocket's vault. Since the two Deoxys had no family, Organism No. 2 thought of Edge as its ancestor and sought after him. But back when it first appeared, Deoxys could only communicate by fighting. Edge realizes that the sensation he felt every time he saw Organism No. 2 was his blood calling out to him. Bayley, unable to keep her eyes open, states that she's glad she was able to give Edge the information in time. Bayley is then fully absorbed by the black hole, causing her fishing line, with Chuchu's Poké Ball attached, to break off the fishing pole.

Edge tells Organism No. 2 that he now understands what it meant by stating that it is him. He claims that Organism No. 2's communication did shake him up, although he states that he was only kidding. Edge hops into the pilot's seat and grabs the airship's steering wheel. Edge tells Organism No. 2 that he feels honored that someone needs his help, no matter what form they're in. Edge notes that although it was captured by Giovanni, he gives it the offer to leave Giovanni or even join his team. Edge tells Organism No. 2 that now that they have had a battle, they're friends now.

Edge sends out Azumarill, Gyarados, Snorlax, Aerodactyl, Charizard, Pikachu, and Chuchu. Edge notes that he's only ridden a bicycle before, so he will have to pilot the airship by imitating what he saw before. He tells the Pokémon that he will handle piloting the airship while they will have to take care of Carr's ten Forretress. Suddenly, text appears on the computer in front of Edge, which is revealed to be Organism No. 2 using its psychic powers. With Organism No. 2's help, Azumarill, Gyarados, Pikachu, and Chuchu locate the first three Forretress and defeat them.

Edge notices Robyn and the others attempting to stop the airship from crashing. Organism No. 2 uses its powers to determine the location of the remaining Forretress. Snorlax, Charizard, and Aerodactyl defeat the seventh, eighth, and ninth Forretress. Organism No. 2 finds the last one, which is hiding in the airship's armory. Edge realizes that if the Forretress uses Explosion in the weapon-filled armory, the airship will be completely destroyed by the chain reaction. Edge rips off his shirt and uses it to bind the airship's steering wheel. Edge tells Organism No. 2 to use its powers to tell the other Pokémon to stay put while they go and stop the Forretress themselves.

At Five Island, Bill and Celio listen to the news report of what's going on in Vermilion City. The townspeople note how even if he stops the airship from crashing, the people might shun Edge just like they did. Seeing how determined Edge is despite the possibly of such a situation like that happening causes the townspeople to cheer for Edge's success.

Back on the airship, Edge and Organism No. 2 find Carr's last Forretress in the armory. The Forretress tries to retaliate, but Edge notices that it is scared, since using Explosion could kill it. Edge tells the Forretress that its Trainer isn't here at the moment, so it doesn't have to listen to Carr's orders. The Forretress briefly wonders about Edge's offer, only to jump and use Explosion anyway. Organism No. 2 jumps in the way of the attack, which doesn't affect it. Edge reveals that beforehand, he had Organism No. 2 take a Poliwrath's (that was one of the wild Pokémon at Vermilion City watching the airship along with the townspeople) Damp Ability with Skill Swap, preventing Explosion from working. Edge praises the Forretress for executing its orders without the need to kill itself.

From the computer, Organism No. 2 asks Edge what kind of creature he is. Organism No. 2 notes that Edge refuses to give up, regardless of whether the situation seems hopeless or how injured he is. Edge simply replies by pulling out his Pokédex and states that he's a Pokédex holder from Pallet Town—the **Fighter**. Edge's shirt rips apart, causing the airship to swerve out of control without a pilot. Robyn notes that they can't keep it balanced any longer and that the airship is going to crash.

Suddenly, the airship begins floating, slides down a building, and lands on the ground almost completely unharmed. Edge stumbles out of the airship and thanks Robyn and the others for their help. Robyn acts confused, as he thought that the airship was stopped by Edge since their attacks couldn't hold it any longer. The five Pokédex holders meet up once more as Mew flies over them.

Azumarill, Gyarados, Snorlax, Aerodactyl, Charizard, Pikachu, and Chuchu come out from the Team Rocket airship and reunite with their Trainers. Organism No. 2 also emerges from the wreckage, much to Robyn and Roberta's shock. Edge and Organism No. 2 shake hands, causing Robyn and Roberta to let out a sigh of relief.

Mewtwo notices Mew flying away and realizes that it was the one who had stopped the airship from crashing. He wonders if Mew had come because it could sense that it was there. Mewtwo notes that where it came from caused it some distress in the past, but since it was created from Mew's eyelash, it has a place where it can trace its roots back to. Mewtwo tells Organism No. 2 that it's glad that it could find someone else who shared the same opinion.

Robyn states that he's glad to see that Edge is alright. Edge thanks Robyn and Roberta for their help, but doesn't know Martinez's name to give a proper thanks to him. Robyn introduces Martinez to Edge and tells him that he did a good job as well. Robyn tells Martinez that he will need more of his help and reveals that according to Giovanni's book, Rhydon can evolve further through trading. Martinez investigates the book and takes the offer with his specialty in Pokémon trading.

When Edge notices the sleeping Bayley, Roberta suggests giving her the empty Pokédex that survived the battle in the Trainer Tower. Edge gives Bayley the Pokédex, officially making her a Pokédex holder. Roberta notes that this feels like a Pokédex holder reunion with all five together. Roberta reveals that she heard of two other Pokédex holders in Hoenn and suggests meeting up with them as well as the other two from Johto.

When Organism No. 2 begins moving, Edge asks where it's going. Organism No. 2, through Edge's Pokédex, reveals that it intends on finding the Deoxys that was discarded by Team Rocket, Organism No. 1. In addition, Organism No. 2 knows that a meteor from outer space is located in a faraway region. With this meteor, Organism No. 2 intends on using it to remove its inability to change its Formes at will. Organism No. 2 turns into its Attack Forme and gives Edge a word of thanks. Edge gives a thanks back, and Organism No. 2 flies off into the air. Suddenly, someone approaches from behind. Meanwhile, outside of Vermilion City, Ultima claims that the incident is over now. Lorelei states that it isn't, as Sird is somewhere nearby. Lorelei has her Jynx create an ice voodoo doll of Sird as payback for what she did earlier.

The person that approached from behind is revealed to be Sird, who is still heavily injured from falling out of the airship. Sird expresses surprise to see how long the Pokédex holders managed to last, especially Bayley, who can increase her team's strength by communing with them. Robyn notes that Sird would never understand how Bayley works, as she only measures strength in numbers. Sird realizes that Pokédex holders' strength comes from their bond with each other, which is why they're so strong. Sird suggests getting rid of the Pokédex holders, but notes that she's too weak to even stand right now.

A ring of ice surrounds Sird's leg, which causes it to freeze over. Sird expresses annoyance at Lorelei's tactic, which she states will take all her strength to break free from. Sird pulls out a Poké Ball and reveals that she intends on capturing Organism No. 2 before it escapes. Edge, with Bayley in his arms, Robyn, Roberta, Martinez, and Mewtwo all jump in front of the Poké Ball as it releases a light. Suddenly, the five Trainers become covered in a grayish-stone color. Sird notes that although she didn't capture Organism No. 2, she managed to get something equal in return. Sird breaks the ice around her legs and leaves while bidding goodbye to the Pokédex holders for the last time.

Professor Oak, Ultima, and Lorelei arrive, having seen the whole thing. Professor Oak asks Lorelei to not let Roberta's parents know about what just happened. At Five Island, Bill gets a call on his Pokégear and tells everyone that the airship has been stopped from crashing into Vermilion City. Although the townspeople celebrate, Bill reveals that the Pokédex holders have been petrified after being engulfed by a strange light. Professor Oak, Ultima and Lorelei sadly stare at Edge, Bayley, Roberta, Robyn and Martinez as stone statues.