Physicists Leonard and Sheldon find their nerd-centric social circle with pals Howard and Raj expanding when aspiring actress Penny moves in next door.
Penny is worried with how damaged her friendship with the guys will be in the aftermath of her sleeping with Raj while Sheldon becomes the leader of the paintball team.
Sheldon's mother, Mary Cooper, comes to visit, but Sheldon is annoyed that she also spends time with the rest of the gang, instead of catering to his every demand.
Leonard and Penny try hanging out as friends on a 'non-date', but end up purposely ruining each others chances with perspective dates. Meanwhile, Sheldon enlists the help of Bernadette and Amy to overcome his fear of birds.
Sheldon gets in trouble with Amy when he isn't impressed by her recent accomplishment, and Howard must come to grips with Bernadette's dislike of children.
Leonard and Penny deal with the idea of starting a relationship again and Raj finally finds a "woman" he can talk to without being drunk, in the form of Siri on his new phone. Meanwhile, Sheldon decides to start a YouTube series entitled "Sheldon Cooper presents Fun with Flags" with the help of Amy.
Sheldon becomes agitated when his regular barber is out sick. Astronaut training causes Howard to reconsider wanting to go into space. Penny beats Leonard in chess, the first time she plays.
Penny buys Leonard and Sheldon “Star Trek” collectibles as a thank-you, leading Sheldon to be haunted by Mr. Spock. Meanwhile, Raj decides he has met the “Future Mrs. Koothrappali” after his parents set him up on a date.
When NASA moves up Howard's mission, he must face his fears and Bernadette's dad, thus putting the wedding plans in jeopardy. Meanwhile, Leonard says something surprising to Penny in the bedroom.
The fifth season ends with Howard and Bernadette deciding to get married before his NASA mission, causing the gang to scurry into overdrive in an effort to stage the wedding. NASA astronaut Mike Massimino has a cameo as himself.