After learning that the person he seeks is in his very own hometown, the Team Rocket leader Giovanni announces that Viridian City will be their next destination, and the TR helicopter begins its way back to the mainland of Kanto.

Standing next to Giovanni, Deoxys drops the hankerchief the man gave him earlier, and Jagura slowly creeps over to pick it up. The little man beckons Storc over, and says he has something important to ask her. Holding up the hankerchief, he demands to know if the person whom their leader seeks is the owner of the item, but Storc simply puts on a cold look and offers him no reply.

Jagura grits his teeth in anger and urges Storc to reveal what she knows, then pulls out the photo which he picked up at the Team Rocket Warehouse on Five Island, stating that if he isn't mistaken, the hankerchief's owner is the red haired kid in the picture, whom he guesses to be the rumoured lost son of their leader.

Storc giggles that she has no idea why Jagura is making such a big deal out of it, and wonders what problem there is if the reason behind their capturing of Deoxys is to find their leader's son. Jagura squeezes his fist in fury, and grunts that it is a big problem to him, because if their boss is indeed searching for his lost son, it means that he plans to pass on the Team Rocket leader title to the boy.

However, a while ago, Giovanni has promised them that he will select the next TR leader among one of the Beast Warrior Trio, which is why Jagura has worked so hard all along to prove his worth. Now that he knows their leader is simply using them for family purpose, he feels cheated and finds it completely unacceptable.

With that, he lets out a howl, and orders a pin missile from his Forretress. But Storc remains calm, and simply raises both of her arms. In a flash of light, the four tentacles of Deoxys come shooting under Storc's arms to strike at Jagura and Forretress, and faint them both with one hit. As the two collapse to the ground, Storc giggles devilishly, and Deoxys slowly withdraws its tentacles. Giovanni is pleased that Deoxys is starting to show loyalty to him, and remarks that it seems to have completely grown accustomed to being a trainer Pokémon.

The TR leader then tells Storc to lock Jagura up in the store room, and the tall woman bows to accept her order. Oca offers to help and picks Jagura up with one arm, and follows Storc's lead to the back of the helicopter. Storc wants Oca to learn his lesson from Jagura, and warns him not to even think about rebellion, but the big man assures her not to worry about him, and says he has no interest in that at all. Tossing Jagura into the store room, Oca states that he is in fact happy for their leader to have found his son, because he always believes that family is the most important thing.

Meanwhile, at the Trainer Tower on Seven Island, Red and his companions continue to struggle with the Deoxys-Divides while Mewtwo remains restrained by the M2 Bind. Green wants confirmation that Deoxys is no longer in the tower, and Red states that he can no longer feel the uneasy sensation in him which arises everytime the creature is around, indicating that it has already left.

After a moment of thought, Green announces that he shall be the director to execute the strategy they have just agreed on. He tells Mewtwo that although he knows it only confides in Blaine, Red and Yellow, it will have to include him in its trust list for now, since he will be the one giving commands. Mewtwo agrees, and Green instantly starts hearing the genetic Pokémon's voice in his head.

Standing back to back with Mewtwo, Green informs it of what he plans to do, while Charizard uses its flamethrower to ward off all the Deoxys-Divides charging towards them. The Trainer Tower's mother computer 'r' chuckles that whatever they do will only end up in vain, and rolls its eye up in mockery.

After explaining his strategy to Mewtwo, Green wants it to remain where it is, and yells out to Red on the other side of the room, asking him to trade Saur with his Charizard. Red gets baffled as to what Green has in mind, but decides to comply since his companion is in charge, and quickly retrieves his Venusaur to commence the trade.

With Charizard now on Red's side and Saur on Green's side, the two Pokémon resume fighting down the Deoxys-Divides, and Green offers his explanation. He states that Red's full team of Pokémon were injured badly in their battle against Deoxys the day before, and are all on the verge of death. With no PokémonCenters available to restore their health and heal their wounds, they are honestly in no condition to fight.

His Venusaur, Saur, is of no exception. While it can still manage to stand its ground, there is no doubt that its usual fighting capacity has been greatly reduced, and it would be the weakest among all three starters which are needed for their current strategy. For their plan to work however, it is important that all three ultimate attacks bear the same power. Clearly, the power intensities of Charizard and Blastoise's attacks must be adjusted with reference to Venusaur's, and as the director, Green believes that it would be easier for him to control the three attacks with Venusaur under his command.

Mewtwo watches Charizard standing behind Red, ready to unleash the fire ultimate attack, while Saur positions itself next to Green, preparing to deliver the grass ultimate attack, and muses to itself how the boys' names and the elemental types they command create the perfect match of fire red and leaf green.

With Red and himself ready, Green calls Blue via his Pokégear, and wonders if she could come back from her floor which is directly below theirs. The girl grunts that it doesn't seem too feasible, and dodges another attack from the Deoxys-Divides while her Pokémon struggle fend them off.

Green states that she must fire off the water ultimate attack from where she is in that case, and tells her to aim the attack directly upwards to blast through the ceiling. Blue immediately orders Turtley to initiate its hydrocannon, and the powerful jets of water easily cracks the concrete ceiling, reaching up to the floor where Red and Green are.

Green then commands frenzyplant from Saur while Red has Charizard unleash its blastburn, and the three attacks all shoot up towards the building's central opening at the roof top like pillars of energy. 'r' laughs that it serves no purpose for them to attack an opening, and says they should perhaps learn how to target their attacks first. But Green pays no heed to its words, and notices that hydrocannon's power is significantly weaker since it comes from a lower floor. He tells Red to slightly tone down the force on his side, and wants to know if Blue can increase hers. The girl replies that she will try her best, and encourages Turtley to give its best shot.

However, while the Blastoise manages to raise the intensity of its water jets, the reaction force starts to push it backwards as well, and it struggles to keep its stance. Blue quickly orders Jiggly, Nidory and Snubbull to support Turtley's weight from behind, but Prof. Oak points out that the three small Pokémon won't be able to withstand the force for too long.

Blue grins that she still has something else planned, and remarks that she has actually been hoping to get back the Pokédex for some time now, since it would allow her to demonstrate the skills she specializes in. Being the Evolver, she has good knowledge and control of the evolution timing and means of all Pokémon.

Just then, Snubbull begins to tremble and glow, and in a flash of light, evolves into a Granbull. Blue next pulls out two moonstones, and tosses them to Jiggly and Nidory, who instantly evolve into a Wigglytuff and Nidoqueen upon contact with the powers of the evolutionary stones. Blue hollers that it is time to abandon their old bodies and embrace their new forms, and voices her encouragement as her three newly evolved team members use all their might to support Turtley.

On the floor above, Green sees that hydrocannon has been powered up, and the intensities of all three attacks are now equal. He tells Blue to angle her attack at 70 degrees towards north, and wants Red to aim blastburn on the same spot. He himself then commands Saur to position its frenzyplant there as well, and signals to Mewtwo. The genetic Pokémon swiftly leaps into the air, and throws itself right at the junction where the three ultimate attacks meet, instantly causing a big explosion which shakes the entire Trainer Tower.

'r' chuckles that it didn't expect Mewtwo to be foolish enough to kill itself, but suddenly hears Mewtwo's voice resounding in its system. It quickly looks over to where the explosion took place, and to its horror, sees that only the remains of the M2 Bind lay scattered around, and the dead body of the genetic Pokémon is nowhere to be seen.

'r' knows that it is in great trouble now, and looks out from the window to see Mewtwo suspending itself in the air with its psychic spoon in hand. The mother computer does not understand how the Pokémon managed to free itself from the M2 Bind and leave the building, and Mewtwo sneers that a computer who is as clever as it claims should be able to figure it out.

However, Mewtwo gives no chance for 'r' to think. Swiping his psychic spoon diagonally across the highest two floors of the Trainer Tower, it slices the building into two, and the top segment falls vertical down to the ground next to the lower portion. The impact slowly shuts down the entire computer system, and seals off all the openings in the building including the one on the roof top. At the end, 'r' manages to figure out how the three ultimate attacks destroyed the M2 Bind without harming Mewtwo, but it gets disconnected from its power source before it could finish its sentence.

While Mewtwo split the Trainer Tower into two, Red has flown out on Charizard, and is now looking down from above at the collapsed top part of the building. With the roof top's opening closed and its bottom sealed off by the ground, most of the Deoxys-Divides are trapped inside with nowhere to go. Red rejoices at their success, but then discovers that he and Mewtwo are alone. He wonders where Green, Blue and Prof. Oak are, and a jet of water suddenly shoots something out from the bottom segment of the Trainer Tower. Red catches it to see that it is the new and upgraded Pokédex, and Mewtwo tells him not to waste the efforts of his friends.

The genetic Pokémon beckons at Red, and the boy knows that his top priority right now is to chase after Giovanni and Deoxys and defeat the two. Holding tight onto Charizard, Red hovers alongside Mewtwo, and prepares to head off to his final battle…

Thanks To Coronis For Writing this for us