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.
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.
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.
Leonard angers the University and the Physics Community when he gives an embarrassing radio interview. Bernadette and Amy compare their successes at work.
Amy and Howard work in the lab together causing Sheldon, Bernadette and Raj to feel jealous and lonely. Penny starts using a parenting book to control Sheldon's behavior.
Sheldon and Wil Wheaton both go head-to-head for the role of the new Professor Proton, Meanwhile Penny takes care of Halley when Bernadette and Howard are on bed rest.
When Bert asks Sheldon to collaborate on a project with him, Sheldon becomes worried about others finding out because he thinks geology is beneath him. Raj seeks advice after reconnecting with Ruchi.
Howard and Leonard become upset after they discover that Sheldon has been working with the military without telling them; Bernadette asks Raj to investigate her suspicions that Ruchi is attempting to take her job away from her.
Sheldon and Amy try to eliminate stress from wedding planning by applying math to the process. Raj and Howard come to blows when Raj begins to feel like Howard hurts his confidence.
Raj and Howard's feud continues as the gang plan Halley's first birthday party. Sheldon's surprise for Amy's birthday goes awry when they get food poisoning.