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After learning Sheldon went behind their backs to work with the military again, Leonard and Howard say Sheldon is like Thomas Edison, taking credit for others' ideas, while they are more like Nikola Tesla. Leonard and Howard bring in Barry Kripke to help create a better idea than Sheldon's, but Kripke goes to the military himself, cutting all three of them out. Meanwhile, Bernadette fears Ruchi is trying to steal her projects at work while she is on maternity leave and enlists Raj to spy on her. Though he finds proof that Ruchi may be stealing from Bernadette, Raj tries to defend Ruchi like a boyfriend would, pointing out Bernadette's hypocrisy as she would most likely have stolen from other people's projects as well. Ruchi is not happy about this and promptly dumps Raj.
When Penny tells Leonard he needs to be more assertive in making decisions for himself, he starts standing up to Sheldon over small things. His confidence makes him want to demand the university support his idea for a plasma physics project. He threatens to quit if the university refuses, alarming both Sheldon and Penny, who consider this to be a risky career move. Sheldon is conflicted on whether or not he is being selfish over Leonard's decision, but Amy suggests that the fact that he is worried over Leonard's motivation proves that he does care about him, which he acknowledges. President Seibert refuses the project, but in order not to lose Leonard, gives him co-leadership over a photon entanglement project, leaving Leonard proud of himself and Penny impressed. Meanwhile, Raj shows Anu his lab, and suggests one possible answer for something he's seen in space might be alien life. When someone mentions this at his observatory presentation, the scientific community starts mocking him as a conspiracy theorist. Raj points out scientists should consider all possibilities when seeking the truth, though this causes people to think he believes in the Loch Ness Monster.
Through the use of his vanity cards at the end of episodes, Lorre alleged that the program had been plagiarized by a show produced and aired in Belarus. Officially titled Теоретики (The Theorists), the show features "clones" of the main characters, a similar opening sequence, and what appears to be a very close Russian translation of the scripts. Lorre expressed annoyance and described his inquiry with the Warner Bros. legal department about options. The television production company and station's close relationship with the Belarus government was cited as the reason that any attempt to claim copyright infringement would be in vain because the company copying the episodes is operated by the government.
Star Trek in particular is frequently referenced and Sheldon identifies strongly with the character of Spock, so much so that when he is given a used napkin signed by Leonard Nimoy as a Christmas gift from Penny he is overwhelmed with excitement and gratitude ("I possess the DNA of Leonard Nimoy?!"). Star Trek: The Original Series cast member George Takei has made a cameo, and Leonard Nimoy made a cameo as the voice of Sheldon's vintage Mr. Spock action figure (both cameos were in dream sequences). Star Trek: The Next Generation cast members Brent Spiner and LeVar Burton have had cameos as themselves, while Wil Wheaton has a recurring role as a fictionalized version of himself. Leonard and Sheldon have had conversations in the Klingon language.
Leonard tells Zack and Marissa he will father their child, but Penny tries to seduce him despite knowing he has to be abstinent for a few days. Her visiting father, Wyatt, points out her actions suggest she is more conflicted over having kids than she lets on, which she admits. Wyatt says he will support her no matter what. Meanwhile, Sheldon and Amy warn that he will not be allowed to raise a child that is not his. Leonard decides not to go through with it; he tells Zack to have Sheldon be the donor, but Amy forbids it. Meanwhile, Howard turns Raj's cancelled bachelor party into a couples' trip into a zero-gravity aircraft, though he's convinced that Bernadette would hate it. Bernadette tries to get out of it so Howard sits out, forcing Bernadette to go through with it just to prove him wrong, though she does not enjoy it.
"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.