Lucky confronts and berates Elizabeth and Nikolas in January 2010. On Valentine's Day, Elizabeth goes to the church they said their vows at, and passes out from hypothermia. Lucky finds her, and when they get to the hospital they learn she is pregnant. Not knowing which brother is the father, Elizabeth has to be talked down off the roof by Lucky, and is sent to Shadybrook sanitarium. The paternity test reveals the baby is Lucky's, but Nikolas' grandmother, Helena switches the results to say it is Nikolas. Nikolas tries to pressure Elizabeth into moving in with him, but she refuses. In July 2010, Elizabeth gives birth to Aiden who is kidnapped by Franco before Lucky finds him. While Elizabeth is distracted by reading the results of another DNA test for Aiden, Jake is hit by a car and dies. Elizabeth has to be convinced by Lucky and Jason to allow Jake's kidney to be donated to Josslyn Jacks. It is soon learned that Lucky's father Luke Spencer hit Jake, under the influence of alcohol. Liz almost interrupts Lucky's green card wedding to Siobhan McKenna to tell him about Aiden, but stops when she realizes that Lucky is happy.
Elizabeth begins hallucinating Jake and messing up at work. Meanwhile, Lucky burns down the Spencer house out of devastation from his father's alcoholic downward spiral. Siobhan is accidentally hurt in the fire, and during her surgery Elizabeth is mistakenly administers the wrong medication. Afterwards, Elizabeth finds Lucky about to drink and tells him that Aiden is his son. However Nikolas does not believe her and plans to take Aiden out of the country. He changes his mind at the last minute and returns Aiden to Elizabeth before saying goodbye to Lucky and leaving town. When the medication error is found out, Siobhan believes it was intentional and tensions between Elizabeth and Siobhan run high. Lucky takes on a drug ring case and is shot up with drugs by order of Anthony Zacchara in an attempt to get him to fall off the wagon. Elizabeth finds him, and while retrieving medication she fights with Siobhan, leading to a car accident. Elizabeth finds Lucky at the church where they said their vows and gives him the medication. Siobhan survives surgery, but later is poisoned to death by Anthony Zacchara. Elizabeth attempts to reconcile with Lucky, but he refuses and leaves town.
Elizabeth accompanies Matt Hunter to a boat party where Lisa Niles throws her overboard, and a mysterious man saves her. Lucky returns home as Aiden is diagnosed with a rare blood disorder. Once he recovers, Elizabeth continues trying to reunite with Lucky and checks into Shadybrook to get his attention, but he refuses and leaves town again. Elizabeth starts spending time with Dr. Ewen Keenan and they go on a few dates. Meanwhile, when Jason sees Sam kissing John McBain, Jason impulsively kisses Elizabeth, but pulls away and apologizes. In fall 2012, Ewen is revealed to be working with Jerry Jacks, who is poisoning the water supply. Ewen kidnaps Elizabeth but Jason saves her by killing Ewen. On Jason's birthday, Elizabeth kisses him again, but Jason says they have no future together. Later Elizabeth gives Jason the wrong DNA test results, falsely telling him that Sam's baby was really dead. Elizabeth hopes to get Jason back, and lies to Sam, prompting her to sign their divorce papers. However, Elizabeth is filled with guilt and comes clean to Jason and Sam. Soon after, Jason is presumed dead, and Elizabeth is heartbroken. Meanwhile, student nurse Sabrina Santiago mentions the Nurses' Ball to Elizabeth, and they make plans to revive the ball. She continues helping Sabrina plan the Ball, as well as giving her dating advice.