Amy agrees to continue living with Sheldon. Sheldon eventually agreed to compromise with Amy by not forcing her to follow a bathroom schedule and sharing a toothbrush holder with her.
When Amy is offered a research fellowship at Princeton for the summer, she is unsure if she can leave Sheldon for three months. After Amy finally tells Sheldon, he insists she must go and tries to be a supportive boyfriend for her, leading to their first non-Birthday coitus. While Amy is in New Jersey, Ramona Nowitzki - the grad student who had a huge crush on Sheldon - returns to Caltech and starts spending a lot of time with Sheldon. As a result, Sheldon immediately flies to New Jersey to propose to Amy.
Leonard and Penny have a second wedding ceremony for their friends and family who are in town. After the ceremony goes off without a hitch, Leonard and Penny are pleased that their families are heading home without incident.
Leonard and Penny adjust to their new-found freedom when Sheldon moves out of the apartment to live with Amy. When Penny feels like Leonard is no longer making an effort in their relationship, she goes on a spa weekend without him.
Leonard travels to the spa to make things right and they both agree that Sheldon should write up a relationship agreement for them. Amy's desire to have an intimate night with Sheldon on her birthday is interrupted by Bernadette going into labor.
After spending the holidays apart, the gang get together to hear about Sheldon's and Amy's trip to Texas, Leonard's and Penny's Christmas tree adventure, and Howard's and Bernadette's first days as parents.
Leonard and Penny ask for Sheldon's and Amy's help on putting the romance back in their marriage. Howard and Raj go to extreme lengths to stop the floor in Halley's bedroom from making noise. Penny wants to help her brother get a job with her company. Sheldon learns of a machine that will help him understand human emotions. Raj reunites some of his old girlfriends to figure out why he is still single. Leonard and Howard's attempt to keep Sheldon away from their Air Force project by sending him on a train trip backfires.
Penny and Amy take Bernadette for her first night out since having the baby. Sheldon and Amy have their first fight since moving in together.
Meanwhile Raj is shocked at the reality of financial independence when he stops receiving support from his father. The guys' annual trip to Comic Con is in doubt when Raj can't afford to go. When the gang offer places for Raj to live, it creates unexpected conflict among everyone. Leonard, Penny and Raj adjust to their new living arrangements; Sheldon expresses an interest in Amy's work. Sheldon reaches his limit when he works on projects with Leonard, Howard and Amy in one day.
Bernadette has doubts about leaving Halley when she goes back to work. Howard and Bernadette have a hard time leaving Halley in daycare when Bernadette returns to work. Bert introduces the gang to his new girlfriend. Leonard is less than thrilled when Penny considers accepting a job offer from her ex-boyfriend, Zack. Sheldon worries that he hasn't reached his full potential soon enough. After celebrating the completion of the top-secret Air Force project, Leonard, Sheldon and Howard get an unwelcome surprise; Amy receives an offer for a summer position at Princeton as a visiting researcher.
The gang become concerned when Sheldon's former admirer, Ramona Nowitzki, resurfaces while Amy is away at Princeton. See also TV Schedule. In order to remain Sheldon's roomie, Amy fibs about repairs being made to her apartment.
Later, they present an episode of 'Fun With Flags' in Penny's apartment.. A successful gene experimentation leaves Sheldon excited to procreate with Amy, and he pulls out all stops to get her on board.
Meanwhile, Koothrappali is reluctant to reveal what the new woman in his life does for a living. A geologist coworker's MacArthur Genius fellowship award leaves Sheldon stone cold jealous. Meanwhile, Howard stumbles upon a remote-control Stephen Hawking action figure that he invented.
Hawking appears as himself.
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