To recruit actors for his rehearsals, Nathan opens an acting studio in Los Angeles, teaching 'the Fielder Method', which involves covertly observing and imitating unaware subjects. Feeling insecure about his own performance, Nathan reenacts the class with actors and a fake Nathan as the teacher while the real Nathan plays the role of Thomas, a student. Nathan makes his students immerse themselves in other people's lives while he immerses himself in Thomas's life, even living in Thomas's home.
Nathan returns to Oregon, where his 'son', Adam, is now a teenager. Nathan and Joshua, the actor playing Adam, decide that Adam should lash out due to resentment of his absentee father and develop a drug problem, a situation that mirrors Angela's own past. Adam suffers an overdose and is tended to by emergency responders played by Thomas and another Fielder Method graduate. After he runs away from home, the 15-year-old Adam reverts to a 6-year-old since Nathan plans to relive his son's earlier years.

Nathan decides to practice his own assertiveness in relationships by challenging Angela over their son's religious upbringing. Angela, a fervent Christian, refuses to allow Adam to be raised in Nathan's Jewish faith, so Nathan secretly brings his son to lessons with a tutor in Judaism under the pretense of swimming lessons. Seeking solace outside the house, Nathan opens his replica Alligator Lounge to the public under the name Nate's Lizard Lounge. The co-parents argue over a comedy skit featuring six-year-old Adam as 'Dr. Fart' and a joke about eating faeces, which Angela claims is a Satanic practice.
Nathan rehearses the confrontations with a fake Angela, and in one scenario, she harshly criticizes Nathan's emotional detachment and questions the ethics of the entire production. However, in their real final confrontation, Angela simply decides to quit the rehearsal. Nathan continues to raise Adam, now as a single parent.

Nathan stages a ninth birthday party for Adam, but faces a problem when Remy, one of the child actors who played Adam at age six, becomes attached to Nathan, calling him 'daddy' even after his scenes are over. Remy's mother explains that her son might have trouble understanding the difference between acting and reality. To discover what went wrong, Nathan repeats Remy's scenes with different actors including Liam (a nine-year-old Adam actor), an adult actor, and a mannequin. He then explores what might have happened if Angela had stayed with him and meets with the real Angela, who urges him to forgive himself, as her religious beliefs state.
In an attempt to truly understand the connection between parent and child, Nathan stages a new scenario in which he is Remy's mother Amber and Liam portrays Remy. They re-create the experience of appearing on The Rehearsal and becoming attached to 'pretend daddy' Nathan. After coming to the emotional realization that they should not have done the show, Nathan as Amber seemingly breaks character and tells the fake Remy, 'I'm your daddy.'