Inside the Trainer Tower on the northern coast of Seven Island, Red, Green and Blue find themselves face to face with a whole gang of flying humanoids after having successfully rescued Prof. Oak and Blue's parents. Though with an appearance as the normal form of the DNA Pokémon, Deoxys, the dull purple creatures lack the crystalline organ on their chests and have hollow eyes.

Green wonders if they are yet another form of Deoxys, and asks Red why there are such a large number of them. But Red has no idea what they are either, and states that he did not encounter such creatures during his fight with Deoxys. Suddenly, the humanoid beings start charging towards the young trainers, and Blue immediately orders Jiggly, Clef, Nidory and Bull to protect Prof. Oak and her parents, while sending out Turtley alongside with Red's Saur and Green's Charizard to fight the creatures. The three starters throw themselves against the massive swarm of Deoxys lookalikes, and instantly engage in a fierce battle with them.

Outside, Brinca, the Sea Gallop sailor and Lorelei, who is still unconscious, are staying airbourne on the old lady's Dragonite. While they have originally planned to enter the Trainer Tower and help the young trainers, the Unowns knocked out by Mewtwo earlier have recovered and are once again fending off intruders to the building. Dragonite unleashes a hyperbeam to blast off a swarm of Unowns in front of it, and Brinca thrashes her staff around to swat them down one by one.

The Sea Gallop sailor wonders if Red and the others have really entered the tower, and Brinca states that she saw it with her very own eyes. After three metal arm extensors threatened to capture Red, Green and Blue into separate glass domes, Mewtwo saved them all and took them into the building as a group. The sailor isn't convinced that Brinca was really able to see all of those from such a far distance, but Brinca tells him not to question her words, and brags that her visual acuity is 6.0, far better than any other old woman at her age.

Brinca adds that the three Team Rocket secret agents who called themselves the Beast Warrior Trio were probably scheming to break up Red, Green and Blue, so that they could have 1 on 1 battles with them. But then she hears Lorelei voicing her disagreement to that, and turns around to see the young woman struggling to sit up after having finally regained consciousness. Brinca joyfully greets her as the ice queen of the elite 4, and feels grateful that she has come around.

Lorelei quickly says she is honoured to have a legendary trainer like Brinca know who she is, and thanks the old lady for taking care of her all this time. Brinca grins that they should leave all the humble words for later, and wants to know why Lorelei disagreed to her idea. Lorelei explains that after she lost to Storc of the Beast Warrior Trio on Seven Island, her Jynx managed to leave a thin layer of ice around the TR secret agent's left ankle, which in fact acts like a tracer to monitor Storc's whereabouts. She opens up her compact mirror which displays a small electronic map, and a flashing spot shows that the Beast Warrior Trio, or at least Storc, are currently not in the Trainer Tower, but somewhere up in the air above the oceans surrounding Six Island instead.

Just then, an Unown charges down towards the Sea Gallop sailor, but Brinca swiftly swings her staff down, and knocks out the symbol Pokémon. Looking intently at the flashing spot on her compact mirror, Lorelei comments that it is moving with such a high speed that the Beast Warrior Trio aren't likely to be travelling on Pokémon. Rather, they are most likely flying in some sort of giant plane.

Meanwhile, a giant olive green coloured battle airship with two rotors on its sides is soaring across the skies towards Six Island. Up on the top of the aircraft, Storc and Jagura are standing inside a fenced area in the open air, and soon spot their fallen companion, Oca, near the coastline as the island comes into view. Storc tells Jagura to retrieve the big man, and Jagura sends out his Steelix to plunge down and scoop him up together with his Shuckle. Once on board the airship, Oca regains consciousness, and the three secret agents proceed to start on the next part of their plan.

Back in the skies outside the Trainer Tower, Brinca remarks that she really didn't expect the Beast Warrior Trio not to be inside the building, and recalls seeing Red, Green and Blue's VS Seekers giving off light beams when they neared Seven Island, which indicates the presence of someone with a battle will against all three of them. The Sea Gallop sailor is curious to know who it could be, and Brinca states that it is probably the question on all of their minds right now.

Inside the Trainer Tower, Saur, Charizard and Turtley are having a hard time dealing with the Deoxys lookalikes, and Red wonders what they really are. Suddenly, a familiar voice comes on to utter the term Deoxys-Divides, and explains that they are clones created by Deoxys which act as its shadows. The voice adds that it is an ability newly learnt by the Deoxys after becoming his Pokémon, and the three young trainers turn around to see the silhouette of a dark attired man hovering on a Crobat. Reciting the phrase Raid On the City, Knock out, Evil Tusks, which essentially is what Rocket stands for, the man reveals himself to be no other than the Team Rocket's leader, Giovanni.

Red, Green and Blue gasp at the appearance of their old foe, and Giovanni grins that it really has been a long time since his big showdown with Red at the Viridian Gym. Just then, several Deoxys-Divides get blasted across the room, and Giovanni looks over to greet his special guest, Mewtwo, who glares at him with furious eyes.

Without a word, Mewtwo swings its psychic spoon at Giovanni, but the man has seen it coming, and bends down adeptly to evade the hit. Landing on the corridor next to the young trainers, Giovanni smirks that it isn't the proper attitude to treat one's creator, and Mewtwo grunts in bitter memory that it certainly will not forget the dreadful process of its creation. Giovanni is amused that Mewtwo has now mastered the skill of telepathy, and Mewtwo hollers that while it only reaches out to people it trusts normally, Giovanni is the exceptional case because it needs him to know the fury it holds against the mastermind behind its creation, the mastermind who created it just for the sake of evil deeds.

Hardly losing his poise at the genetic Pokémon's accusations, Giovanni is curious to know why it is there now, and Mewtwo declares that it will not permit him to cause another Pokémon the same misery it went through, and shall stop his evil schemes with all its might. Blinded by rage, Mewtwo leaps up and prepares to strike down with its psychic spoon, but three of the Deoxys-Divides cut in the way to block the attack, and Mewtwo jumps back in frustration.

Baffled by the conversation between Mewtwo and Giovanni, Red rushes over to Mewtwo and wants to know what it means by saving another Pokémon from the same misery. He wonders if Mewtwo has learnt of a Pokémon created in the same fashion as itself by Team Rocket, and Mewtwo states that Red has in fact met the Pokémon in question already. It tells Red to recall what kind of Pokémon Deoxys is, and Red remembers Jagura once referring to it as the DNA Pokémon. Mewtwo explains that DNA, which is short for deoxyribonucleic acid, is the basic building block of all living things, and makes up the genetic material of all beings. Since Mewtwo itself is known as the genetic Pokémon, and both DNA Pokémon and genetic Pokémon basically share the same meaning, it has feared that Team Rocket is repeating their evil schemes ever since it learnt of the existence of Deoxys.

Listening to Mewtwo's explanation, Giovanni is impressed that Mewtwo is intelligent enough to draw such a sound comparison between itself and Deoxys, but is sure that it does not know what really happened. The man decides that there is no point in keeping it a secret anymore, and reveals that Deoxys was in fact a Pokémon mutated from a space virus as a result of exposure to laser beams, making it a one of a kind species which possesses the unknown powers of the outer space.

Red, Green and Blue gasp at the revelation of Deoxys's creation, and finds it hard to believe that it actually came from space. Giovanni laughs that he has failed to control the will of Mewtwo, and thus resorted to seek what he needs from Deoxys instead. Right now, he possesses all the unknown powers of outer space in his hands, and shall achive his goal in no time.

Mewtwo turns red with fury from Giovanni's words, and vows to make him pay for what he did. However, the TR leader is less than worried, and remarks that he has already taken safety precautions in handling Mewtwo's deadly powers. Giovanni clicks on a button on a remote control in his right hand, and the high-tech machines in the room without warning shoot out metal arm extensors to trap the genetic Pokémon inside a white armour.

Red bolts with shock, and hurries over to help Mewtwo, but the white armour refuses to bulge, and Giovanni smirks that it is a specially designed device to restrain Mewtwo known as the M2 Bind. He adds that he has no idea where Mewtwo learnt of his current work, but it's obviously its misfortune to have learnt it.

Meanwhile, on Five Island, Bill has managed to fix the island's Pokemon Storage and Transfer System, and exits from the PokemonCenter. He wonders where Red and the others are now, and feels a little upset that they left him behind. But then he reminds himself that he has his own duties as well, and suddenly hears someone calling him. He turns around to find Celio running towards him, and is glad that his colleague is all well amid the current havoc of the Sevii Islands.

Celio explains that he managed to escape from the rampaging residents on One Island, and has travelled over on his motor boat. He apologizes for leaving Bill to work on things alone all this time, but Bill assures him that it is alright, and is grateful that he is there to join him now. Bill then suggests contacting the two girls as soon as possible, and Celio says he knows where to find a phone.

At the Hoenn Branch Pokemon Storage and Transfer Management Center, the phone goes off, and Lanette rushes over to pick up. However, she accidentally knocks over a huge pile of books and gets herself buried in them. She quickly climbs out from her mess and answers the call properly, while her elder sister, Bridgette, sweatdrops at her clumsy behaviour…

Thanks To Coronis For Writing this for us