"You know I am in love with you."
-Bart to Lily, Roman Holiday
In The Wild Brunch, Dan overhears an argument between Bart and Lily at the Bass' Annual Brunch about their relationship and whether to become public. Lily catches him and asks him not to tell Serena; and he agrees. In The Handmaiden's Tale, Lily invites Rufus to Eleanor Waldorf's Night in Tangiers party to make Bart jealous. The plan works when Bart sees the two kissing, and asks for a moment alone with Lily. In Victor Victrola, Chuck fails at proving himself to his father and inadvertently tells Lily that he saw Bart out with a young, attractive woman. Lily has no problem believing Bart was unfaithful to her, and begins to ignore him. Chuck comes clean to Bart about what he did, and Bart seeks to earn her forgiveness.
In Roman Holiday, Lily finally tells Serena and Eric about her relationship with Bart. They aren't happy, but try and accept him into their lives. On Christmas morning, Bart proposes to Lily. During spring break, Lily, Serena, and Eric move in with Bart and Chuck. In Woman on the Verge, Bart and Lily host their rehearsal dinner but the festivities are interrupted when Serena's biggest secret comes out. In order to help her daughter, Lily leaves the dinner early and escorts her to find closure; which includes stopping at Rufus' concert. After seeing him perform, the two end up spending the night together at a hotel. In the season finale Much 'I Do' About Nothing, Lily prepares for her wedding to Bart. He asks her once and for all to let Rufus go, and she agrees to. They end up marrying and plan to spend the summer renovating her penthouse.
Bart and Lily return from their vacation in The Ex-Files, and Lily happily shares little stories from their time together but turns to Rufus when she learns that being with Bart is lonely. In The Serena Also Rises, Lily attempts to buy a painting of herself but discovers that Bart already did. She assumes it was purchased as a present, but finds out that he bought it to keep anyone from finding it; and that he learned about it via a private investigator he hired to create a dossier about her. In Chuck In Real Life, Bart and Lily create rules for Serena, Eric, and Chuck to abide by. Chuck discovers that they're planning to transform their family to close a business deal, and Serena decides to rebel by ruining their party. After talking with Dan, she decides to give the family a chance and Bart and Lily agree to be more honest on who their family really is.
In The Magnificent Archibalds, Eric discovers that Bart has files on him, Serena, and Lily. He tells Lily, and the fact that Bart keeps files on her children angers her. They leave before Thanksgiving Dinner and spend the holiday with the Humphrey's instead. In It's a Wonderful Lie, Lily has decides to leave Bart for Rufus. They dance at The Snowflake Ball, and Chuck calls Bart to tell him. On the way to the dance, Bart gets into a car accident and dies. In O Brother, Where Bart Thou?, Lily finally listens to a voicemail Bart left her the night he died. In it he reveals he knows the true reason she was hospitalized in France.
After Bart is revealed to still be alive (Raiders of the Lost Art), Lily learns she has to annul her marriage to Rufus or Bart, as they never divorced before his "death". In The Return of the Ring, Rufus has annulment papers drawn up behind Lily's back and she is angered when she finds out. She ultimately chooses to annul her marriage to Rufus and stay married to Bart.
When Chuck brings his new friend Amira to the VDW penthouse to rattle Bart in High Infidelity, Lily discovers she had an affair with Bart. In Portrait of a Lady Alexander, Lily lies to Bart at Chuck's request and Bart follows them. He confronts her about it, then asks her to stay away from Chuck. She refuses, saying Chuck is her son too.
In Where the Vile Things Are, Lily accidentally auctions off the painting where Bart is hiding the records of his illegal oil deals. She, Chuck, and Ivy bid against one another but ultimately lose to Rufus. In Save the Last Chance, Ivy promises the records to either Bart or Chuck and says that whoever ruins Lily's life the worst can have them. Bart plans to divorce her, but Ivy thinks the plan is too soft. She tries to set up Bart to make it look like they slept together, but is stopped when Chuck arrives; and Lily gets the records thanks to Rufus and ends the ordeal. In It's Really Complicated, Lily learns of the death of Bass business manager, Bruce Caplan. Blair and Chuck link his death along with Sheikh Hassan's back to Bart and Bass Industries, and Lily realizes she was wrong for trusting Bart over Chuck and heads out of town for a spa week. In the series finale New York, I Love You XOXO, she learns of Bart's death while still at the spa and returns to town to have a funeral the same as the first.