Lily works at the Pokémon HQ Lab in Orre. While there, she works on one of the main projects, the Purify Chamber. At the start of the game, she will send the player to find Jovi, who's run off to Kaminko's House. After Jovi is found, Lily sends Michael and Jovi to Gateon Port to get the Machine Part to finish the machine. After Professor Krane is kidnapped by Naps, she pushes to finish the Purify Chamber. After the chamber is finished, she will remain in the room supporting the chamber for the remainder of the game.
According to an NPC, Lily was considered to be a very popular student in the past, and many boys competed to impress her, including Professor Krane and the man who would eventually win her heart and become Michael's father.