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.

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.
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.
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