The film returns to the forties. Allie returns to Noah and the two take a boat ride and are caught in a thunderstorm. Allie asked Noah about why he did not write her, and he reveals that he did. Noah and Allie make love into the night. The next day, Allie's mother appears on Noah's doorstep, telling Allie that the jealous Lon has followed her to Seabrook. After a confrontation turned heart-to-heart, Allie's mother returns the bundle of Noah's 365 hidden letters. When alone, Noah confronts Allie about what she is going to do; Allie confesses that she doesn't know. and once again, they fight. Noah asks her to ignore what he, or Lon, or her parents want and asks, again and again, "What do YOU want?" Confused, unable to answer his question, Allie returns to the hotel. On the way she stops and reads the last of his letters, She confesses to Lon, who is angry but admits that he still loves her. He tells her that he does not want to convince his fiancée that she should be with him, but Allie tells him he does not have to, because she already knows she should be with him but, tellingly, not that she WILL be with him.
The film picks up the now lifelong lovers, as "Duke" asks Allie whom she chose. She realizes the answer herself, that the "story" he was reading was their story; young Allie appears at Noah's doorstep, having left Lon at the hotel and chosen Noah. They embrace in reunion. Elderly Allie suddenly remembers her past before she and Noah/Duke joyfully spend a brief intimate moment together; after originally finding out about her illness, she herself had written their story in the notebook with the instructions for Noah to, "read this to me, and I'll come back to you." But soon Allie relapses, losing her memories of Noah yet again. She panics, and has to be sedated by the physician. This proves to be too difficult for Noah and he breaks down. The next morning, Noah is found unconscious in bed and is rushed to the hospital; he later returns to the nursing home's intensive care ward. He goes to Allie's room later that night, and Allie remembers again. When Allie questions Noah about when she won't be able to remember anything anymore, he reassures her that he will never leave her. She then asks him if he thinks their love for each other is strong enough to 'take them away together.' He states that he thinks their love could do anything. After telling each other that they love one another, they both go to sleep in Allie's bed. The next morning, a nurse finds them in bed together, having both died in each others' arms.