Lily was kept out of sight till 2004 when she returned to Pine Valley after threatening to run away from school. She agreed to live with Jackson and his new extended family after a decision was made to allow her to attend public high school. Lily managed to adapt well to the new system until a group of girls began harassing her. Spiking her drink with alcohol among other things, Aidan Devane came to Lily's rescue when the "hot girls" spray-painted her with red paint which debilitated her. This led her to have her first crush and she asked Aidan to be her boyfriend. Jackson was livid when he found out about this and confronted Aidan but was appeased when he realized that Lily was the one who liked him, and not the other way around. Aidan accepted Lily's request to be her pretend boyfriend, a role that she said would only require his being there to talk and play math games. Hoping to be a positive influence on her, Aidan played along.
Soon, Lily's feelings turned romantic and she asked Danielle Frye and Erica Kane for advice who attempted to dissuade her. Aidan also tried to get her to understand that nothing could happen between them, but it didn't work. Hurt and confused when she witnessed him kissing Anita Santos, she ran away to the Wildwind barn, where she witnessed the murder of Edmund Grey. Before Lily could do anything, the barn caught on fire and she would have died, had it not been for Aidan.
Lily suffered from post traumatic stress and retreated back into herself with the knowledge of the crime she had witnessed on her shoulders. While all of Pine Valley thought Zach Slater had been the one to kill Edmund, she slowly began to reveal that it had actually been one of Ryan Lavery's brothers - though she didn't say which. It was around this time that everyone began to suspect Braden Lavery of poisoning his sister-in-law, Greenlee Smythe, and of killing Edmund. Worried about his children, Jackson sent them away with one of Aidan's friends, Steve, to Lily's old school, but were stopped when a tire blew. Greenlee and Lily took cover among the trees before they heard a noise and went to see what the matter was. Steve was gone, but Jonathan Lavery was there brandishing a gun. He told Greenlee that it was all part of a plan to help Ryan. He would hold the girls and make Braden pretend he was on his side. Things ended horribly when a bomb went off in the cave, leaving Jonathan dead - but everyone else was unharmed.
Lily had a real but short-lived romance with Sam Grey, the adopted son of Maria Santos Grey and the late Edmund Grey. He was closer to her age, but didn't understand the triggers of her disorder. It ended before the Grey family moved to California.
Lily married Jonathan, but the marriage was later annulled when it was revealed that Jonathan had recovered from his brain tumor. Lily's half-sister Ava Benton, came to town to meet her for the first time. After Ava left town, Lily was offered to be a student at the Massachusetts Institute of Technology, which she accepts, and Lily left town to start life anew.