Carr pilots the Team Rocket airship with the intent on killing everyone else on board. Sird and Orm try to get to the cockpit and stop Carr, but Orm slips and falls off into the trees below. The force knocks the airship's controller from Red's hands, which Sird takes with her Persian's Thief. Sird uses the controller to deactivate the airship's stadium mode and states that she has to get control of the airship before Carr crashes it.
Now safe, Red and Mewtwo head towards the cockpit. Red takes Organism No. 2 with him, as he states that he can't leave it behind while it's injured. Red attempts to shake the door open, but Carr states that nothing he will do will get it open. Sird appears before Carr on a video phone, but he states that nothing she can do will be able to stop him. Suddenly, Sird's Starmie appears, having used Camouflage to disguise itself as a wall. Starmie knocks Carr and the pilot's seat off of its position.
Sird tells Carr that she will not allow him to mess with Giovanni's reunion with his son. Carr praises Sird's tactics, but claims that he's better. A huge explosion rips a hole in the airship, sending Sird and one of Carr's Forretress flying out of it. Carr reveals that he planted ten other Forretress on the ship and commanded them all to use Explosion so that if the ship lands safely, it will still be blown up. Carr escapes from the airship on his Skarmory and flies off.
Mewtwo breaks the door down and states that they have to get off the airship immediately. Red states that they can't, as the Forretress could severely damage a town or city if they crash and then blow it up. In addition to that, Silver and Giovanni are still on board as well. Red asks Yellow to help him, but she begins dozing off from overusing her powers. Red realizes that this was Sird's intention when she told Yellow to use her powers on Organism No. 2. Mewtwo states that although it agrees with him, it asks Red what they should do. As it approaches Vermilion City, the airship tips over.
At the Safari Zone, the warden and Pidgebot watch as the ship flies above them. In Vermilion City, the people of the Pokémon Fan Club rush outside to see what's going on. At the docks, the Sailor announces that they have arrived at Vermilion City. Blue and Ultima quickly realize that the crashing airship is the one they were after. Green asks Lorelei who's still on the ship. Using her tracking mist, Lorelei determines that Sird isn't on it. Blue tries calling Red on his Pokégear, but gets no response. Blue and Green immediately rush after the airship in order to try and contain the damage.
Back on the airship, Red states that he has a plan, but will need Organism No. 2's help. He has Organism No. 2 create a black hole to send Silver and Giovanni somewhere else. Once they're safe, he sends Yellow and Mewtwo into it as well. Mewtwo tries to stop him, but Red points out that the black hole is only an entrance to an exit. Mewtwo states that's not what it was talking about and asks what Red is planning to do. Red smiles and tells Yellow and Mewtwo that he will return safely as they continue to be engulfed.