In the episode "The Launch Acceleration", Amy tries to use her "neurobiology bag of tricks" to increase the attraction between herself and Sheldon. In the final fifth-season episode "The Countdown Reflection", Sheldon takes Amy's hand as Howard is launched into space. In the sixth season first episode "The Date Night Variable", after a dinner in which Sheldon fails to live up to this expectation, Amy gives Sheldon an ultimatum that their relationship is over unless he tells her something from his heart. Amy accepts Sheldon's romantic speech even after learning that it is a line from the first Spider-Man movie. In "The Cooper/Kripke Inversion" Sheldon states that he has been working on his discomfort about physical contact and admits that "it's a possibility" that he could one day have sex with Amy. Amy is revealed to have similar feelings in "The Love Spell Potential". Sheldon explains that he never thought about intimacy with anyone before Amy.
Like the previous three seasons, the first five episodes aired on Mondays due to CBS' contractual rights to air the Thursday Night Football games. After Thursday Night Football ended, the series returned to a Thursday schedule starting on November 2, 2017. Filming for the eleventh season began on August 15, 2017; it was also announced with the taping report that the premiere for the eleventh season would be titled "The Proposal Proposal". Before the season premiered, five episodes were filmed from August 15 to September 19, 2017.
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.
Anu wants to have sex with Raj, but he gets so nervous in the leadup, that his selective mutism returns. Confessing to her, she is very understanding, revealing an unusual secret of her own. The next morning, he is able to have sex with her in the shower. Sheldon attempts to bond with his father-in-law, but Larry is more impressed with Howard's magic tricks, causing a jealous Sheldon to spend time with Mrs. Fowler. They bond after finding out Amy has been using Sheldon as an excuse to avoid her mother, though he does gently advise her to forgive her daughter like he would his wife. A remorseful Amy invites the Fowlers over for thanksgiving, where Sheldon and Mrs. Fowler continue to bond over Larry's ineptitude with magic.
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.
Sheldon is annoyed that Amy does not have time to work on the super-asymmetry project with him so he talks President Siebert into getting her removed from her own project at the university. Amy is angry at both of them as she wants to still have her own identity outside the marriage. When confronted by Amy, Siebert apologizes to her but states that it will be difficult for the university to give her her project back. After talking with Arthur Jeffries in a dream, Sheldon apologizes to Amy and both of them talk about their fears in their marriage. Meanwhile, Raj does not want to have Howard join him in his show at the planetarium, thinking he'd just use his astronaut status to make it about himself. Raj eventually lets him join in and Raj and Howard spend the whole time complimenting each other, surprising Bernadette, Leonard and Penny.
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.