Mewtwo, with Red, Blue, and Green riding in its barrier ball, flies towards the large cluster of 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.
Blue 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, Red realizes that they are at the Trainer Tower, where Trainers attempt to battle their way to the top. Red decides to start defeating their opponents, but Blue and Green 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 Red and Mewtwo notice that they are simply holograms. Several mechanical clamps shoot up from the tower's spheres and capture Red, Blue, and Green. Mewtwo easily slices through the clamps with its spoon and moves everyone down with its powers. Red gets angry that Team Rocket used Blue and Green's family to trick them, but Mewtwo states that its their fault for falling for the enemies' trick.
Red 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. Blue immediately sends out his entire team to rescue his grandfather. Blue tries to have Scizor cut off the shackles, but an invisible wall stops the attack. A voice tells Blue that the system is immune to Pokémon attacks.
The voice is revealed to be R, the computer of the Trainer Tower. Red is shocked to see that the tower is alive, Blue 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, Blue attempts to prove it wrong.
R notices something quick has entered its network system. The thing is revealed to be Blue's Porygon2, who moves to R's nervous system at an incredible speed thanks to its Salac Berry. Porygon2 uses Zap Cannon, which fries R from the inside, defeating it. Blue has Porygon2 release his grandfather from his shackles. Blue then has Porygon2 use Recycle to reuse its Salac Berry so that it can release Green's parents from their shackles. Mewtwo points to another room, which has Green's parents held inside, now freed from their shackles. Green has a tearful reunion with her parents, but it's interrupted by several silhouettes who appear in front of the group.