Just after the player has returned home, a live [[television]] broadcast from Aether Paradise is interrupted when Team Rainbow Rocket makes its entrance there, taking over Lusamine's mansion. When the player arrives to Aether Paradise with Lillie, they find out that Team Rainbow Rocket has taken Lusamine hostage and turned her mansion into their base; [[Team Rocket's Castle]]. Upon trying to enter the castle, the player and Lillie are confronted by Faba, who is revealed to have allied himself with the villainous team in the hopes of furthering his own career.
Once Faba has been defeated, the player starts making their way through the castle. Along the way to rescue Lusamine, they must battle and defeat the villainous team leaders [[Archie]], [[Maxie]], [[Cyrus]], [[Lysandre]], and [[Ghetsis]] whom Team Rainbow Rocket had summoned from alternate universes where their respective plans had succeeded. At the deepest part of the castle, the player confronts the team's leader, [[Giovanni]], who reveals his goal being to assemble an army of Ultra Beasts using Aether Foundation's resources. However, once the player has defeated him, he accepts his loss and leaves, causing the mansion to be restored to normal in the process. Faba is punished for his treachery by being demoted to an intern, and Giovanni is seen teleporting away to continue his evil schemes in a different reality.