After seeing Atlas in the present and learning he has a girlfriend, a job, and a stable life, Lily decides that finishing the old journal may give her the closure she needs. She resumes reading entries addressed to Ellen DeGeneres, returning to the period when teenage Lily was secretly helping homeless Atlas.

In the first entries, Atlas becomes severely ill after climbing through Lily’s window. Lily gives Atlas medicine, water, her bed, and care through a night of vomiting, then pretends to be sick so Atlas can stay in her room the next day while Lily’s mother is at work. Their closeness deepens as they watch Finding Nemo, and the phrase 'just keep swimming' becomes a private symbol of endurance between them.

Atlas later tells Lily that Atlas has contacted an uncle in Boston who may let Atlas live with him. Lily feels torn between happiness for Atlas’s safety and fear of losing Atlas. That night, their intimacy shifts when Atlas thanks Lily, touches Lily tenderly, and gives Lily her first kiss; afterward, neither of them discusses Boston.

Over the following week, Lily and Atlas begin kissing daily and grow increasingly attached. When Katie mocks Atlas on the bus for his clothes, Lily is furious, but Atlas asks Lily not to respond; Lily instead reassures Atlas that Atlas is her favorite person. At Lily’s house, Atlas cooks cookies during a power outage, showing Lily a caring, competent side of manhood unlike Lily’s father, and later gives Lily a small wooden heart carved from the oak in Lily’s yard. Lily treasures the gift but fears it is a goodbye token before Atlas leaves for Boston.

The journal then turns darker: Lily’s father comes home drunk and attacks Lily’s mother after accusing her of flirting. Lily finds him on top of her mother and reaches for a knife, but Atlas stops Lily and plans to call the police. Lily’s battered mother refuses, insists the police would make things worse, and denies the attempted assault as something Lily is too young to understand. Atlas leaves, and Lily helps her mother clean up, realizing her mother copes by refusing to acknowledge painful truths.

In the final entry Lily reads, Atlas is leaving for Boston despite briefly considering staying to protect Lily. Lily encourages Atlas to go because Atlas needs a home, and Atlas describes Boston with longing, making Lily promise that she may someday move there and find him. Back in the present, Lily stops before the last journal entry, puts the diary away, and tells herself that both Lily and Atlas are happy now. Lily then reads vulnerable texts from Ryle about relationships feeling like a reward rather than a burden, and a proud text from Lily’s mother about Lily’s business and doctor boyfriend.