She gives the player character the task of saving Cosmog. The Cosmog, nicknamed Nebby, is suddenly attacked by three Spearow and then the player character arrives. Cosmog escaped her bag and she gets worried. Three months later, Lillie is encountered going to the Ruins of Conflict. Professor Kukui took her in and gave her a place to stay. She is found by Professor Burnet at the beach and she tells her husband. She is cornered by three employees, but Cosmog teleported them out of the paradise. Lillie is first seen in the intro of the game three months before the story takes place, fleeing from Aether Paradise. Lillie can be found near the Ten Carat Hill entrance on Saturday evenings staring at the night sky with something in her bag. The name Lillie originates from 'lily' as her white dress resembles the white petals of a lily flower as well as the name following the plant-based naming of characters.

Lillie also decides to go to Kanto to become a true Pokémon Trainer so that she may earn badges and meet and catch lots of wonderful Pokémon. Lillie eventually decides to travel to Kanto to find Bill so that he may give her the cure for Nihilego's poison. After Lusamine gets separated from Nihilego, she regains some of her sanity back and touches Lillie's cheek. When the player character and Lillie meet Lusamine in Ultra Space, she gets the courage to yell at Lusamine for being terrible for trying to control her and stating that 'children are not just things that belong to their parents'. She became unbearable to Lillie, so she left as well. However, over time, Lusamine started becoming insane and grew even madder when Gladion escaped Aether Foundation two years before the story begins. Lillie originally had a close relationship with her mother, as she mentioned sleeping in Lusamine's bed as a child. This happens usually because Lillie is trying to avoid Team Skull grunts, as she is not a trainer, and ended up going in the wrong directions trying to get away from them. Lillie is always getting lost, and the player character has to help her. When she is traveling with the player character, she is usually exclaiming to do some shopping of her own, and in cities would tell the player character that she got lost and ended up buying outfits in a shop. Lillie was revealed to have taken a Cosmog from her mother, and along with Kukui and Burnet are studying the Cosmog and its secrets.

She's not fond of making Pokémon fight in battles, but she loves reading and has devoured many books. Lillie is a mysterious girl who assists the professor for personal reasons.

Nanu pokemon smile