Professor Proton, Sheldon's favorite childhood show, is being rebooted. After unsuccessfully auditioning for the part, he goes to Wil Wheaton for acting tips for his second audition. However, Sheldon is later dismayed when Wil is offered the role instead. Talking it over with Arthur in his dreams, he is still upset to see his idol replaced and considers Wil an enemy again. Meanwhile, Howard gets a vasectomy while Bernadette is on bed rest. Penny offers to take care of Halley for them, but they insult her by expecting her to be irresponsible. Halley ends up saying her first word by calling Penny "Mama."
Howard and Bernadette learn their second child will be a boy, leading Howard to doubt whether he can be a good father to a son. He and Sheldon go out in the desert to test launch a model rocket, but it explodes, causing him further doubt. On the way home, Howard does a good job coaching Sheldon to drive them home, for which Sheldon tells him he will be a good teacher to his son. Leonard's mother Beverly begins talking to Penny as a friend and confidant, troubling Leonard, especially when he learns that Beverly told Penny that she was proud of her, a level of praise she never bestowed upon Leonard himself. When Leonard confronts Beverly, he is touched when she says that of all of her children's spouses, Penny is the one by whom she is most impressed and that, for this, she is indeed proud of him. Meanwhile, Raj helps Bernadette turn baby girl clothes into boy ones.
Although the original pilot was not picked up, its creators were given an opportunity to retool it and produce a second pilot. They brought in the remaining cast and retooled the show to its final format. Katie was replaced by Penny (Kaley Cuoco). The original unaired pilot has never been officially released, but it has circulated on the Internet. On the evolution of the show, Chuck Lorre said, "We did the 'Big Bang Pilot' about two and a half years ago, and it sucked ... but there were two remarkable things that worked perfectly, and that was Johnny and Jim. We rewrote the thing entirely and then we were blessed with Kaley and Simon and Kunal." As to whether the world will ever see the original pilot on a future DVD release, Lorre said, "Wow, that would be something. We will see. Show your failures..."
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.