Lusamine berates both Lillie and Gladion for leaving and stealing from her, after all the love she gave them, and shows no care for either of them. After raiding the facility, whose employees have now become hostile to them under the pretext that there are intruders, the player manages to enter the house and office of Lusamine, its president, where they find Lillie trying to reason with her, finding out as well that Lillie is Lusamine's daughter, and that Gladion is her brother, who had also ran away from Aether Paradise for similar reasons. He takes them to Aether Paradise, where he claims he is certain Lillie has been brought. Upon informing the player about this, Gladion, a Team Skull enforcer that the player and Hau have encountered several times, who has warned them to ensure nothing happens to Nebby, barges in, having overheard the conversation. The reason for this is revealed much later on, while they are on Ula'ula Island: while staying at the Aether House on Route 15, Lillie and Nebby are kidnapped by Team Skull in an operation led by Plumeria, who implies that Team Skull are not the only ones who steal Pokémon at this, Lillie goes with them willingly and quietly, while Hau is unable to defeat Plumeria to save her. Notably, she does not join the player and Hau in their tour of Aether Paradise. She and the Professor travel to the Ruins of Life to watch Kahuna Olivia and Hau battle when Hau reminds the player that Faba of the Aether Foundation wants to see them, Lillie becomes nervous and insists on staying to watch the battle. She rejoins the player and Hau when Professor Kukui summons them to the Dimensional Research Lab, which conducts research into Pokémon coming from other dimensions and is headed by Professor Burnet. She also tells the player that, in her quest to learn more about Nebby, she would like to visit each of the ruins of Alola where the guardian deities live. Throughout the player's and Hau's journey on Akala Island, Lillie mostly stays at the Tide Song Hotel in Heahea City, apparently to meet somebody there, and also in fear of Team Skull, who she saw lurking around the area. After the player defeats Kahuna Hala, she goes to Akala Island alongside the player and Hau. After the player completes their first trial, Nebby escapes from her bag and runs off into Melemele Meadow, so the player must find it and return it back to her. After assisting the player at the Trainers' School, she visits Hau'oli City. Sometime after that, she accompanies the player to Kukui's Lab and later provides them a tour of the Pokémon Center. Afterwards, she accompanies the player back to Iki Town, where she watches them receive their starter, and later their Z-Ring or Z-Power Ring. Despite not yet having a Pokémon of their own, the player steps in to protect Nebby, and is in turn assisted and recognized by Tapu Koko. The player first meets Lillie on the Mahalo Trail, where she watches helplessly as Nebby is being attacked by a group of wild Spearow on an unstable rope bridge. She contacts her husband, Professor Kukui, who allows her to stay with him as his assistant. Lillie and Nebby wash up on a beach, where they are found by Professor Burnet, who listens to Lillie's story and agrees to help her learn more about Nebby. Just when she is surrounded, she is Teleported by a mysterious force, later revealed to be the Pokémon hiding in her bag, Cosmog, which she nicknamed Nebby. Lillie is first seen attempting to flee Aether Paradise three months prior to the beginning of the player's adventure, during the opening cutscene. She dislikes Pokémon battles as she does not like seeing Pokémon get hurt but loves to read.

She assists, and is shown to live with, Professor Kukui for personal reasons. Lillie is first revealed as a mysterious girl who is central to the plot of Pokémon Sun and Moon.

Lillie pokemon smile