Though he is upset, Don manages not to shut down completely; he does, however, decide to get drunk. Gene and Claudia follow him home, but he refuses to let them up. Instead, he returns a happy birthday call from his family and ends up having to correct their secretly long-held belief that he is gay. 

Don recounts all he has learned about himself during the Rosie Project: He is capable of blending in and now understands that everyone else may simply be trying to blend in as well; while he lacks some emotional skills, his attention to detail is a valuable skill that people appreciate; he is capable of having fun and maintaining close relationships; and, realistically, he can have a relationship with a woman. But he still takes Rosie’s words to heart and believes that he isn’t able to love anyone, not even Rosie.

When Don wakes up, he has further, clearer insights. Without consciously realizing it, he resolves the issue that was still bothering him: Rosie’s insinuation that he lacks empathy and the ability to love. He surmises that he does have an ability to empathize, but the situation must involve someone he loves or cares about—not a fictional movie character. He recounts many instances of his empathy, including occasions in his relationships with Daphne, Claudia, and Rosie herself. Even a somewhat compromised ability to empathize does not mean that Don cannot love, because he knows he loves Rosie. He notes difficulties experiencing empathy as a defining characteristic of autism. 

Reinvigorated, Don runs back to find the coat he threw out. He discovers that an unhoused man took his jacket from the trash can, so Don carefully removes his cellphone and the envelope he’d left in the pockets. A couple watches him and, thinking he is robbing an unhoused man, calls the police. Don rides his bike to campus, one step ahead of the police. In his office, he finds that his Father Project file has been ransacked by Rosie, who has left him a note of apology. Afraid that she will confront Gene without DNA proof of paternity, he rushes to locate Gene and head Rosie off. He finds everyone at the University Club—Gene and the dean at one table, Rosie and Claudia at another.

Don rushes up to Rosie and announces that he knows he loves her because everything about her and the way she makes him feel is irrational yet he still wants to marry her. Rosie admits that she was scared of finally having everything she wanted—a relationship with Don—because he is so different than what she’d imagined for herself. Smiling, she presents the ring from the previous night’s proposal, which Don had left on the table. He puts it on her finger, and she agrees to marry him. Don kisses Rosie to the applause of the entire dining room. At that moment, Phil arrives, along with the club manager and two police officers. The club manager points Phil in Gene’s direction, and before anyone can stop him, Phil punches Gene. Even though Don isn’t sure that Gene is Rosie’s father or even slept with her mother, he feels this is retribution for all the men Gene has undoubtedly wronged over the years with his behavior. Before he and Rosie can leave, the police question Don about what he took from the homeless man; he shows them that the envelope contains three tickets to Disneyland.

Don, Phil, and Rosie go to Disneyland. Don and Rosie marry and move to New York City; they decided the move would make it easier for Don to maintain all of the positive changes that he has made because it’s okay to be weird in New York. There, Don works in the genetics department at Columbia University and Rosie attends medical school. They work together three nights a week in a cocktail bar for extra income, and they are planning to have a baby. Don thinks about all his progress: He has developed a love of music (but only for the genre his father listened to while Don was growing up); he can hug Rosie despite his aversion to most physical contact; and he spends one day a week socializing with Dave and other Yankees fans.

Don reveals that, at the wedding, Dr. Hughes approached him with an important detail about Rosie’s mother’s death. Phil had been in the car that night and despite suffering a broken pelvis because of the crash, his first instinct was to rescue Rosie. Don knew that this is something a parent would do, so he is confused about why Phil would do this for Rosie if she wasn’t his biological daughter. 

Some undefined amount of time later, Don asks for permission to use Columbia’s testing facilities for a private matter. He takes the remaining DNA samples from the Father Project, plus the sample taken from Phil, and tests them. Before confirming his theory, Don texts Rosie so that she can be there to see the results. Don’s suspicions were correct: Phil is Rosie’s biological father. 

Don blames Gene for the entire mix-up. As the professor of the genetics class that Rosie’s mother took as a medical student, Gene vastly simplified his explanation of inherited physical traits, like eye color. Rosie’s mother had no way of knowing that two blue-eyed parents can have a brown-eyed child, so she based the confession of her affair to Phil on incorrect information. Incredulous, Don remarks that, without Gene’s mistake, he would never have met and married Rosie.