Lillie/Games/SM

She requests for its help to save Lusamine in Ultra Space, where she is unfazed by Guzma's claims that Lusamine is beyond reason, and goes to confront her. She finally manages to stand up to her, despite being called ugly for leaving her and befriending the player. After the player defeats Lusamine, who has merged with, she attempts to strike Lillie with one of her tentacles, but Lillie cries out to Nebby for help, who manages to separate Lusamine and Nihilego. Before losing consciousness, Lusamine asks Lillie when she started becoming more beautiful.

Upon returning to Alola, Nebby indicates its desire to join and travel with Lillie, who gently refuses as she is not a Pokémon Trainer. She suggests it join the player instead, who is required to catch it to proceed with the storyline. Lillie then leaves to take care of her mother, and until the player becomes Champion she is not seen, as she is busy caring for Lusamine in Aether Paradise. She does tell Gladion, however, to tell the player that he/she is the "best trainer in the world". During the festivities in Iki Town, Lillie and the player quietly slip away to the Ruins of Conflict to give thanks to ; when they return, she tells the player that Lusamine is getting a bit better, and even wanted to join the party, and that she has been gently helping her understand what she has done. She also stops short of telling the player something seemingly important; this is revealed the next day by Hau, to be her departure for Kanto, where she plans to seek treatment for her mother and become a Trainer in her own right. She gives the player her old Poké Doll and says goodbye to them. She is not seen after this.

After Lillie has left, the player can read her diary in the loft of Professor Kukui's lab, as the lock has been pecked open by. In it, Lillie writes that her flight from Aether Paradise had been planned ahead, with only Wicke aware of it, and that Wicke had told her to look for Professor Burnet. She is seemingly turned off at Professor Kukui's habit of going around half-naked. She also notes that Alola does not have any Gym Leaders or — at that time, toward the start of the player's journey — an Elite Four. Wicke also tells the player, upon their return to Aether Paradise, that the reason Lillie chose Kanto was to seek Bill, who, like Lusamine, has been combined with a Pokémon before, in the hopes that Lusamine would be healed of the last of Nihilego's poisons.