The player meets [[Lysandre]], who tells him/her of the ultimate weapon he managed to create and use in his world, and shows two buttons on the wall, one of them activating the ultimate weapon in this world. He offers the player a chance to save the world or doom it by pressing one of the buttons, but no matter which one the player presses, the ultimate weapon starts charging up, and will only turn off if the other one is pressed. Lysadre fights the player to prevent him/her from doing so, and is defeated.
After the player swipes a key card in Cyrus' office and presses both buttons in Lysandre's office, the door in Lusamine's room opens and the teleporter activates. When the player and Lillie get ready to use it, [[Ghetsis]] suddenly comes out of it. He tells them he
have been summoned to this world to separate people from Pokémon, and is planning to use Team Rainbow Rocket's boss to achieve his goals. A battle ensues and Ghetsis loses. He breaks down, strikes down Lillie and threatens to kill her unless the player gives up on all of his/her Pokémon on the spot.
As the player hesitates to comply, [[Colress]] suddenly reveals himself, having used his inventions to follow the player while remaining invisible and send other villainous leaders back to their worlds.
He berates Ghetsis and teleports him away. He explains to the player and Lillie that what happened to Lusamine's manor is a product of multiple dimensions converging, and he can restore it, but only after the player defeats the leader of the villainous team.
Lillie and the player take the teleporter and are welcomed by the mastermind behind the invasion, [[Giovanni]]. Lillie also discovers Lusamine
, unconscious and, according to Giovanni, brainwashed with an Ultra Beast's toxins. The player fights and defeats Giovanni, who gracefully retreats, but not before promising the player they will meet again. Suddenly, the player and Lillie find themselves in Lusamine's trophy room, the manor having been reverted to its normal appearance. Lusamine wakes up, shaky, but still herself, and Guzma and Colress join them. Amidst the celebration of their victory against Team Rainbow Rocket, Faba suddenly walks from behind one of Lusamine's trophies. He tries sucking up to Lusamine, but gives himself away as a traitor almost immediately and hastily leaves.
The day is saved and Faba has been demoted to an intern. Watching as life at Aether Paradise returns to normal, Giovanni wonders out loud what other worlds he could unleash his schemes upon and teleports away on his own.