Red and Mewtwo arrive at the Team Rocket airship, which has changed shape to put a battlefield on top. Red's body begins quivering again, signaling that Deoxys is waiting for them. Suddenly, several poles shoot beams that become a pyramid-shaped barrier that prevents Red and Mewtwo from escaping. After landing, Red puts Charizard back in its Poké Ball. From the center of the battlefield comes Giovanni and Deoxys on an elevator.
Giovanni welcomes Red and Mewtwo and asks them what it's like to be standing from their position. When Red asks what he's talking about, Giovanni states that since Red was the only one to beat him in battle, he stands on higher ground. Giovanni states that since he is a challenger, he will be facing Red not as the ViridianGym Leader or leader of Team Rocket, but a regular Trainer with no titles. Giovanni throws off his jacket and tells Red, the Champion, to face him. Red takes his jacket off in response, and Giovanni states that the battle will be a one-on-one between Mewtwo and Deoxys.
On the battlefield, Mewtwo introduces itself to Deoxys while the DNA Pokémon remains silent. Although it expresses annoyance at the Deoxys Duplicates it faced at the Trainer Tower, Mewtwo states that it's a pleasure to face it in battle. Immediately, Mewtwo attacks with its spoon, but Deoxys blocks the strike with its tentacles. Mewtwo continues attacking furiously, which causes the battle to quickly move into the air. Mewtwo tells Red that he is free to give it any commands in the battle. Mewtwo rushes in to attack once more, but Deoxys rapidly shifts into its Speed, Defense, and Attack Formes.
Deoxys manages to knock Mewtwo onto the ground. Giovanni reveals that the Ruby and Sapphire's power has reached Viridian, which allows it change Formes at a quick pace and change strategies in an instant. Mewtwo asks Red for a strategy, but he states that he doesn't have one. Since any strategy will be countered by its Forme Change, Red tells Mewtwo that it should attack with the strongest move in its arsenal. Mewtwo fires a blast from its hand and aims at the crystal in Deoxys's chest.