On the Team Rocket airship, Giovanni charts a path to Viridian City to find his son. 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, Blue decides to take the lead on the strategy they discussed since Red can't sense the real Deoxys being there. Blue asks Mewtwo to trust him and allow him to hear its thoughts. Mewtwo decides to allow Blue to hear its thoughts with telepathy. R tells them that they should give up, as it is useless. Blue has Red trade Saur over to him in exchange for his Charizard.
Blue explains that since Red wasn't able to heal his team after the battle with Deoxys, Saur is currently the weakest of the three Pokémon needed in the strategy. Blue states that he will use Saur's current strength as reference and have Charizard and Blasty adjust theirs accordingly. When Blue tells Red to have Charizard use Blast Burn while he has Saur use Frenzy Plant, Mewtwo notes that Red is using fire, while Blue is using leaf. Blue calls to Green and asks her if she can make it up to have Blasty use Hydro Cannon. She states that she can't, so Blue tells her to aim from the floor and break through the ceiling.
Much to R's shock, Green has Blasty break through the floor with Hydro Cannon. Blue and Red follow suit with Saur's Frenzy Plant and Charizard's Blast Burn. Blue tells Red to lower his power while asking Green to increase hers. Green has Blasty increase his power, but it causes him to begin moving backwards from the force of the attack. Snubbull, Nido, and Jiggly try and hold Blasty in place, but Professor Oak states that they aren't strong enough to handle it.
Green reveals that seeing the Pokédex again reminded of her skill as an Evolver. Snubbull immediately evolves into a Granbull, while Jiggly and Nido are given Moon Stones to evolve into Wigglytuff and Nidoqueen, respectively. With their new forms, the three Pokémon help Blasty keep his footing. They focus the three Ultimate Moves upwards into the center. Blue 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. Red 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 Red fly off to face Giovanni in the final battle.
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