Raj hooks up with a recently separated woman, Nell, after one of his lectures at the planetarium. Her husband, Oliver, confronts Raj at the planetarium and then breaks down over the end of his marriage. After comforting Oliver, Raj talks to Nell and convinces her to give her husband another chance. Meanwhile, after diving once again into string theory and sprawling his work across his and Amy's apartment, Sheldon approaches a reluctant Leonard and Penny and convinces them to let him use his old room to study for a three-day trial period with an agreement to be quiet and stay out of their way. Sheldon surprisingly sticks to this agreement, being a reasonably good guest, which shockingly frustrates Leonard to no end. After Leonard lets out his frustrations, Sheldon then renegotiates the guest tenancy agreement for an extra few days and resumes being his normal demanding self, much to Leonard's relief.
Bert asks for Sheldon's help in a geology research project relating to dark matter. Sheldon secretly agrees, but is too embarrassed to admit he is working with rocks. Bert finds out about this and ends their partnership. After talking with Amy, Sheldon goes to apologize, only to find Leonard has taken his place. Meanwhile, Raj runs into Ruchi again and goes out with her, but she does not believe in romantic love. After Howard and Bernadette tell Raj that he can just have sex with Ruchi, he agrees to keep it casual.
"The Locomotive Manipulation" is the first episode in which Sheldon initiates a kiss with Amy. Although initially done in a fit of sarcasm, he discovers that he enjoys the feeling. Consequently, Sheldon slowly starts to open up over the rest of the season, and starts a more intimate relationship with Amy. However, in the season finale, Sheldon leaves temporarily to cope with several changes and Amy becomes distraught. However, in "The Prom Equivalency", he hides in his room to avoid going to a mock prom reenactment with her. In the resulting stand-off, Amy is about to confess that she loves Sheldon, but he surprises her by saying that he loves her too. This prompts Amy to have a panic attack.
When Leonard receives a braggy Christmas letter from his brother, he feels bad about how little he and Penny have achieved in the past year. Leonard wonders if he and Penny should be thinking about the next step after two years of marriage, like buying a house or having a baby. Penny tells him she wants to do all those things someday, but she has a bunch of stuff she would like to do first.