Sheldon and Amy recruit Leonard to research and write citations for their paper on super asymmetry. While working in the campus library, Leonard and Raj discover a Russian paper that asserts that super asymmetry has no merit. Reluctantly, Leonard shares the news with Sheldon and Amy, who fall into a depressive state and do not leave their apartment. Meanwhile, Bernadette asks Denise to teach her how to play Fortnite: Battle Royale so that she can beat Howard. Despite losing to Howard in a rematch after all of her training, Bernadette revels in beating a disinterested Penny.
"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.
"It's different for everybody. It was time for me and I felt that. It's both simple and complicated. I don't have a diary that I could bring out and say, 'Here are the reasons as far as quote-unquote future plans in a concrete way or (that I had) a problem with coming here.' None of those things were true," he says. "I felt it was the right moment for me. But, it only helps so much to go through the end of something like this feeling you've made the right choice. It's still exceedingly emotional."
President Siebert charges Leonard with distributing some extra university funds in the form of a grant. Everyone begins sucking up to Leonard. Penny is impressed by Leonard's decisiveness but unimpressed when he cannot decide between Raj, Kripke and Dr. Lee (Maribeth Monroe), an ornithologist who works with crows. Leonard, realizing that people will be angry with him no matter who he gives the funds to, eventually awards the money to himself; many crows swarm his car afterwards. Meanwhile, a stressed out Bernadette starts hiding in Halley's playhouse after work so she can have time to herself. She is eventually joined by Penny and Amy. Howard reveals to Raj that he actually knows that Bernadette has been hiding out, but is keeping quiet about it so she can have her privacy and so he can use it to his advantage.
Sheldon and Amy are surprised to find that Wil Wheaton's new Professor Proton show is actually very entertaining and that Wil had Howard on as a guest. On Howard's suggestion, Sheldon apologizes to Wil, mending their friendship, and tells him he wants to be on the show; but Wil asks for Amy. Sheldon tells her to do it, but she says she often doesn't do things to avoid upsetting him. Sheldon is horrified when he realises how selfish he has been, especially when he finds out that the men do the same for him. Sheldon encourages Amy to go on the show to inspire girls to pursue science while trying to control his obvious jealousy for her. Meanwhile, Leonard writes a book about a physicist that solves a murder, the protagonist Logan Dean is based on himself. Bernadette points out Logan's mean boss Illsa is similar to Penny, who thinks it is based on Bernadette, though Leonard does not correct her. However, Bernadette tells Penny the truth, upsetting her and making her mad at Leonard. After calling his mother for advice, Leonard learns that Illsa is actually like her; but abandons the book when he realizes he wrote romantic tension into the relationship between the characters.