Elizabeth Afton is first heard in dialogue between the nights. In this dialouge she is heard begging her father to let her see Circus Baby, and eventually sneaks away to see her. Baby's monologue about being on stage, reveals, as Elizabeth was the only one in the room, Baby's programming kicked in and a claw within her grabbed Elizabeth and killed her. The Baby Minigame shows this happen directly. Elizabeth goes on to possesses Baby due to Remnant, however she is not fully in control as the AI of Baby also functions. Her soul ends up within Ennard, and she scoops Micheal, by this point believing him to be William, to be used as a flesh suit.
In the Fake ending, Ennard tries to get at Michael in the Private Room, and uses Elizabeth's voice to emotionally bait him into giving up.
After Ennard ejected themselves from Michael decaying body, Elizabeth, through Baby, urges Michael to not die, which triggers Mike to revive.
Freddy Fazbear's Pizzeria Simulator
After being ejected from Ennard, Baby rebuilds herself as Scrap Baby. After Henry lures her, Molten Freddy, The Marionette, and Springtrap to a fake restaurant, he sets fire the place, and freeing her and the remaining children's spirits. Michael chose to go up in flames with his family, including Elizabeth.