Orm's black Pokédex continues calculating the level of Yellow's Pokémon, which rapidly rises towards the eighties. Orm guesses that Yellow's Pokémon are so attuned to their Trainer, that their levels rise when Yellow gets angry. Although Sird notes how interesting the battle has gotten, she tells Orm to look at the more important matter upwards. Orm looks up and sees that the Team Rocket airship has transformed into its Stadium mode.
They realize that Mewtwo must have pursued them from the Sevii Islands. Silver checks his Silph Scope and sees Deoxys, which he had never seen before. Sird tells him that Deoxys is being controlled by his father, Giovanni. This revelation causes Silver to start stumbling. Silver claims that Sird is lying, but she sends her Banette to knock Silver unconscious. Sird and Orm take this chance to load Silver into the pod while Yellow tries to stop them. When Orm asks why they're simply running away, Sird states that she wants to give Silver to Giovanni before Yellow catches up. Sird states that if they battle with Yellow, she will defeat them.
On the Team Rocket airship, Red tells Mewtwo to just attack the crystal in Deoxys's chest. Deoxys just blocks the attack with its arms. Giovanni expresses disappointment that Red attacked without a plan. Giovanni has Deoxys attack Mewtwo with a barrage of punches. Mewtwo tries to counter-attack, but Deoxys blocks it with its Defense Forme and attacks with its Attack Forme. Giovanni notes that Red specifically attacked Deoxys's chest and asks why he chose that strategy. Red reveals that when Pika used Thunder on Deoxys's chest, it caused Deoxys to stop moving.
Mewtwo rushes into an attack, but Deoxys rushes past it with its Speed Forme. As Deoxys grabs Mewtwo with its tentacles, Giovanni states that Red correctly guessed that the crystal is Deoxys's core. Deoxys continues strangling Mewtwo, but a stray attack shoots down and pierces it through the chest.
Back on Seven Island, Ultima emerges from the rubble of the Trainer Tower. She gets annoyed that everyone forgot about her, but quickly starts falling off a cliff. Lorelei saves her with her Shellder's Icicle Spear, which pins Ultima to the wall. After confirming that Red and Mewtwo have left while Blue and Green are still inside, they decide to regroup with the others. After landing, Lorelei asks Ultima if she managed to get the item she was looking for. Ultima praises Lorelei's intuition and presents the item she was looking for: the Old Sea Map.