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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.
A fight between Sheldon and Penny leaves Amy caught in the middle, while Leonard tries to spice up his long-distance relationship with Priya.
Leonard and Amy get to know each other better, while Howard and Bernadette spend the weekend with Mrs. Wolowitz.
Penny plays Matchmaker for Raj, which results in him finding a girl he is comfortable talking to.
Sheldon and Leonard get invited to a party at Wil Wheaton's house, and Howard gets an out-of-this-world opportunity.
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.
A cute comic book artist puts Leonard and Priya’s relationship to the test, while Sheldon tries to scare the guys for Halloween.
Amy becomes heartbroken when she discovers that Penny and Bernadette went wedding dress shopping without her.
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.
When Stuart asks Amy out on a date, Sheldon must confront his feelings and consider where his relationship with Amy is going.
Leonard must face his fears after being contacted by his high school tormentor.
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, who broke up with Priya, asks Penny out to a spur-of the-moment romantic dinner for two, and the duo contemplates on their relationship.
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's selfish demands force Leonard to reconsider their friendship. Meanwhile, Wolowitz tries to pick his astronaut nickname.
When Sheldon is forced to take his vacation, he goes to work with Amy in her neurobiology lab.
Penny is horrified when Amy gives her a gift: a huge, quite horrible painting of the two of them. With no good way to avoid displaying it, she only hangs it up when Amy is over. When Amy catches her taking the painting down, she's embarrassed and angry until Penny lies and says the gift made Bernadette jealous. When the deranged Professor Rothman is forced to retire, both Sheldon and Kripke vie for his office. President Siebert refuses to resolve the dispute, so Leonard arranges a one-on-one basketball game to decide (since they're both equally bad at sports). Neither one can even make a single basket, so they end up deciding by seeing who can bounce the ball the highest. Sheldon wins; unfortunately, the office is not what he'd hoped for: the thermostat is located in the office of a professor going through the hot flashes of menopause (thus Sheldon is too cold), the mockingbird outside his window is off-key with the annoying windchimes, the perpetually naked Professor Rothman refuses to vacate, and the Geology Department upstairs makes too much noise. Finally, Sheldon gets his head stuck in the wall in an existing hole, after which Leonard takes his picture before he goes for help.
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.
Sheldon must choose between joining Amy at her aunt's birthday party or playing videogames all weekend with the guys.
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 Wolowitz gets to work with Stephen Hawking, Sheldon is willing to do anything to meet his hero.
After the guys throw Howard a bachelor party, Bernadette reconsiders marrying him after learning about his sexual history.
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.