Walkthrough: Once the warp portal has opened in Lusamine's Room, return there and attempt to enter it with Lillie. However, directly before you do, the leader of Team Plasma, Ghetsis, will appear, mentioning he had heard something about intruders. Ghetsis will tell you nothing can stop Giovanni, only to eventually go on to say that he plans on using Giovanni as his pawn so he can actually liberate all Pokemon in order to rule all of the universes. He will then challenge you to battle.
Team Plasma Ghetsis - Level 66 Cofagrigus, Level 66 Bouffalent, Level 66 Bisharp, Level 66 Hydreigon, Level 68 Zekrom
After defeating him, Ghetsis will say that you cannot stop him, going on to threaten Lillie's life if you don't stand down and give him your Pokemon. Before you can react, Colress will suddenly appear out of nowhere using another new device he created, teleporting Ghetsis back to his universe. He will go on to say that Ghetsis hasn't changed one bit, even if that Ghetsis wasn't the one he use to know. He will then tell of his device, how it can send things back to their appropriate universe, citing Necrozma's power and its overflow as to why all of this is happening.