After Sheldon has a food truck moved away from the building, Leonard and Penny are shocked to find he is the leader and sole member of the Tenants' Association for the building. Amy doesn't want to be caught in the middle but secretly suggests they rally support from the other tenants to vote Sheldon out. Nobody else supports Leonard so Amy tells them Sheldon was never added to the lease when he moved across the hall with her. Sheldon fires back with his own legal technicality so Amy is forced to support Leonard. She makes Sheldon happy by saying he can be Leonard's official opposition, making Leonard believe he made a mistake. Meanwhile, Howard and Raj find a drone. Raj returns it to the cute owner Cynthia and gets her number. Unfortunately, Cynthia watches footage of Raj on the drone and is immediately turned off.
Leonard and Sheldon are brilliant physicists—geniuses in the laboratory but socially challenged everywhere else. Enter beautiful, street-smart neighbor Penny, who aims to teach them a thing or two about life. Despite their on-again, off-again relationship in the past, Leonard and Penny have finally gotten married. Even Sheldon has found a female companion, entering into a "relationship agreement" with neurobiologist Amy Farrah Fowler, and he recently took their relationship to the next level by marrying her after a long courtship. In their free time, Leonard and Sheldon enjoy fantasy role-playing games with their ever-expanding universe of friends, including fellow scientists Koothrappali, Wolowitz, and Wolowitz’s adorable microbiologist wife, Bernadette, who is adjusting to life with their two children.
After Neil Gaiman tweets about Stuart's comic book store, it becomes very popular, and the crowds upset Sheldon. Stuart hires an assistant manager named Denise and she impresses Sheldon with her comic recommendations. Amy goes to her for information on comics to connect to Sheldon but when she tries to tell him, he says he's talked enough about comics with Denise. The store's popularity causes Stuart to be unable to babysit for Howard and Bernadette's date night. They try to have another at home, but Stuart shows up so they hurriedly go out. Meanwhile, as Raj sets up a telescope, Penny sees a new comet. Raj takes sole credit for the discovery, angering Penny. Leonard tries to defend her but feels sorry for hurting Raj's career. Penny confronts Raj herself and he agrees to share credit after Penny doesn't give in like Leonard.
Howard dresses as Sheldon for Halloween at work, hurting Sheldon's feelings. When Howard does not apologize, Amy and Sheldon dress as Bernadette and Howard at Penny and Leonard's party, angering Bernadette. Sheldon and Bernadette later bond over their painful childhood memories. Leonard is upset that Penny does not seem to remember that their first kiss was on Halloween. Penny later admits she does remember, but does not like to think of their first kiss as an unromantic drunken hookup. She likes to imagine their first kiss was one they shared on Leonard's birthday, which pleases him.
In the third-season finale, Raj and Howard sign Sheldon up for online dating to find a woman compatible with Sheldon and discover neurobiologist Amy Farrah Fowler. Like him, she has a history of social ineptitude and participates in online dating only to fulfill an agreement with her mother. This spawns a storyline in which Sheldon and Amy communicate daily while insisting to Leonard and Penny that they are not romantically involved. In "The Agreement Dissection", Sheldon and Amy talk in her apartment after a night of dancing and she kisses him on the lips. Instead of getting annoyed, Sheldon says "fascinating" and later asks Amy to be his girlfriend in "The Flaming Spittoon Acquisition". The same night he draws up "The Relationship Agreement" to verify the ground rules of him as her boyfriend and vice versa (similar to his "Roommate Agreement" with Leonard). Amy agrees but later regrets not having had a lawyer read through it.
^ "Editor's Note: With final Monday ratings in, The Big Bang Theory has now reached a new series high in viewers (16.32m) and was the night's top program in adults 18-49 (5.9/15), up a tenth from this morning. -- "Two and a Half Men" Soars to Its Best Adult 18-49 Rating in Three Years". CBS. March 9, 2010. Archived from the original on January 8, 2014. Retrieved January 5, 2013.
Sheldon has been writing to the reclusive scientist Dr. Wolcott (Peter MacNicol) who invites Sheldon to visit him in his completely isolated mountain cabin. The women quickly ask Leonard, Raj and Howard to tag along with him, making this his bachelor party, despite Sheldon's assertions that it shouldn't be called such. Wolcott has a brilliant mind but his behavior is very strange to the guys. He tells Sheldon he cut off all contact with others to focus on science. Though Sheldon enjoys the science, he decides that he doesn't want to live like Wolcott because of his friends and Amy. The guys leave to avoid Wolcott, whose theories about time make him doubt whether the guys were ever there. Meanwhile, Penny and Bernadette throw Amy a quilting bee for her bachelorette party, which she quickly finds boring. When Amy tells them she wants a night full of bad decisions as she earlier implied, they go to a bar where Amy drinks a few shots and passes out in twelve minutes. When she wakes up back at the apartment hungover and disappointed, the women lie and reassure her she had a wild time, involving her drunkenly riverdancing.
After the birth of Michael, Howard and Bernadette are unsure who should stay home with the kids. Howard decides to look after the kids one day to show he has what it takes to care for them. While Bernadette falls back in love with her job on a trip to the office, Howard is quickly tired and realizes he might not have what it takes to be a stay-at-home dad. Howard and Bernadette realize neither them is ready to give up their job.
After Sheldon reminds the guys about the time they mined Bitcoin without him, the guys go on a quest to find their suddenly valuable missing cryptocurrency. They realize the currency is on a laptop which Leonard gave to Penny when they dating, which she then gave to her ex-boyfriend Zack. After Leonard and Penny go to Zack's apartment, he shows them a seven-year-old video that Penny recorded on the laptop soon after she broke up with Leonard. Leonard is touched by the video which shows a drunk Penny lamenting the break-up of her relationship with him.