In the Indigo Plateau's central control room, a confused Gold learns from Crystal that the Magnet Train was used to bring the Gym Leaders to the opening ceremony. Unable to find a way to abort the release of the Magnet Train's security, Gold decides to go back to the stadium for help, but soon finds that he and Crystal are trapped inside. They call out Exbo and Archy to burn the door down, but the door remains intact. Crystal finds that Monlee's Mach Punch doesn't break down the door either. While Crystal thinks hard for another solution, Gold finds a way to contact the rest of the stadium from the control room.
Gold's face appears on the big screen over the stadium, much to the Pokémon Association Chairman's fury. The boy manages to warn the audience about Team Rocket's impending arrival and the Magnet Train being hacked, before the big screen is suddenly interrupted to show the Masked Man's battle with Ho-Oh, causing the audience to panic. By then, Crystal has prepared a mix of spores from Parasee, which, combined with Sludge Bomb, tear a hole through the door. Just as Crystal and Gold break free from the control room, the Magnet Train zooms into the stadium once again.
As the stadium audience evacuates, the Chairman, who has come down from the VIP room along with Bill and Daisy, tries to call for the Magnet Train system to be fixed. At the next moment, the Magnet Train doors bolt open and numerous masked Team Rocket Grunts spill out. Falkner calls the Gym Leaders into action. Blaine arrives back on stage just in time to join the fight against the grunts. When 15 of the 16 Gym Leaders are lured into the Magnet Train, however, its doors slam shut and the train speeds off into the distance.
By now, Gold and Crystal are on their Tibo and Natee respectively, looking over the scene of chaos. They hover towards the announcer's box where Mary and Radio Director Hiro are. They confirm that Gold's message went through, and that the Gym Leaders went on the Magnet Train before it zoomed off. Crystal knows the Gym Leaders' roles, and that they were tricked into entering the train as a means of diverting attention away from their enemy.
A voice duly confirms thus. Gold and Crystal turn around to see that the Masked Man has arrived, with both Lugia and Ho-Oh.