A large crowd of Deoxys surround Red, Blue, and Green. The group wonders why there are so many of them, while Red notes that they only look like Deoxys. The Deoxys begin attacking, so Green has Clefy and Jiggly protect her parents and Professor Oak. The three Trainers send out Saur, Charizard, and Blasty 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 Red, Blue, and Green 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 Red, Blue, and Green 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 Blue. 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, Red, Blue and Green'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, Red, Blue, and Green 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 Red, 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. Red 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.