Bert asks for Sheldon's help in a geology research project relating to dark matter. Sheldon secretly agrees, but is too embarrassed to admit he is working with rocks. Bert finds out about this and ends their partnership. After talking with Amy, Sheldon goes to apologize, only to find Leonard has taken his place. Meanwhile, Raj runs into Ruchi again and goes out with her, but she does not believe in romantic love. After Howard and Bernadette tell Raj that he can just have sex with Ruchi, he agrees to keep it casual.
Howard and Raj are still fighting, so Howard dis-invites Raj to Halley's birthday party. However, when Stuart pulls out as party planner at the last minute, Raj agrees to plan the party, which doesn't turn out too well due to Halley being asleep, Bernadette being on bed rest, and no people turning up. When Howard and Raj get into a shoving match in the party's bounce house, they end up letting out their frustrations, but also having fun and reconciling. Leonard is depressed upon receiving his successful brother's Christmas card and attempts to make a list of what he and Penny accomplished this year, not coming up with much. This prompts them to think about their plans for the future, so they decide to go on trips and achieve more out of life together before starting a family. Sheldon cooks Amy a Little House on the Prairie-themed birthday dinner, which gives them both food poisoning. They eventually recover enough to attend Halley's birthday party with the others, where they have fun in the bouncy castle and then have sex in Howard and Bernadette's house.
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..."
Penny and Bernadette attend a pharmaceuticals conference, where Bernadette's business rival Danny tries to recruit Penny. Bernadette is offended that Penny is considering the offer. At the meeting with Danny, Bernadette steps in to say Penny is the best saleswoman she knows and Penny agrees to keep working for Bernadette. Meanwhile, the rest of the gang does simple behavioral experiments on the Wolowitz children using a book Sheldon found. Leonard is shocked that his childhood was filled with these experiments; although his mother remembers that time with him fondly, she admits the experiment with him is not over. Raj figures Amy planted the book to get Sheldon to like babies, though Sheldon later states he would be open to having kids.
Cosmologist Stephen Hawking made a short guest appearance in the fifth-season episode; in the eighth season, Hawking video conferences with Sheldon and Leonard, and makes another appearance in the 200th episode. In the fifth and sixth seasons, NASA astronaut Michael J. Massimino played himself multiple times in the role of Howard's fellow astronaut. Bill Nye appeared in the seventh and twelfth seasons.
However, no legal action was required to end production of the other show: as soon as it became known that the show was unlicensed, the actors quit and the producers canceled it. Dmitriy Tankovich (who plays Leonard's counterpart, "Seva") said in an interview, "I'm upset. At first, the actors were told all legal issues were resolved. We didn't know it wasn't the case, so when the creators of The Big Bang Theory started talking about the show, I was embarrassed. I can't understand why our people first do, and then think. I consider this to be the rock bottom of my career. And I don't want to take part in a stolen show".
Science has also interfered with the characters' romantic lives. Leslie breaks up with Leonard when he sides with Sheldon in his support for string theory rather than loop quantum gravity. When Leonard joins Sheldon, Raj, and Howard on a three-month Arctic research trip, it separates Leonard and Penny at a time when their relationship is budding. When Bernadette takes an interest in Leonard's work, it makes both Penny and Howard envious and results in Howard confronting Leonard, and Penny asking Sheldon to teach her physics. Sheldon and Amy also briefly end their relationship after an argument over which of their fields is superior.
Two physicists from Chicago, Dr. Campbell and Dr. Pemberton, accidentally prove Sheldon and Amy's super-asymmetry theory. This puts them on track for a Nobel Prize, but Leonard points out they tend to go to the experimental scientists who prove a concept instead of theorists like Sheldon who come up with it. Meeting with them, they tell Sheldon they are willing to share the Prize but only three names can be on the submission, and they want to cut Amy out. Amy does not want to prevent Sheldon's lifelong dream, but he goes to President Seibert who agrees to fight for Amy on their behalf. Meanwhile, Bernadette's drug has been approved and she wants to promote Penny to lead the marketing team. Penny resists, knowing Bernadette's attitude at work and doubting her own inexperience to take the responsibility, but Bernadette uses reverse-psychology to get Penny to take the job. Penny mirrors Bernadette's commanding style to get the other employees in line, impressing Bernadette.
Leonard's mother Beverly visits, and he is thrilled when she takes an interest in his work. However, when he learns that she is doing research on him for a new parenting book, he is furious. He prepares to tell her how she let him down over the years, but instead chooses to accept and forgive her, and forgive himself for holding onto that resentment for so long. Beverley is touched that he forgave her and they share a genuine hug. Meanwhile, Anu gets a job offer in London. Raj prepares to fly out and propose to her, ready to follow her if she accepts. Howard stops Raj at the airport, saying there is a better match out there for him, convincing Raj to return home. Stuart and Denise are bothered by her creepy roommate Mitch, while Bernadette and Howard are tired of Denise constantly staying overnight with Stuart at their house. Stuart says he is ready to move in with Denise, and they say they love each other while convincing Mitch to move out.
^ Kondolojy, Amanda (November 8, 2013). "Thursday Final Ratings: 'Elementary', 'Scandal', 'The Vampire Diaries', & 'The Big Bang Theory' Adjusted Up; 'The Voice', 'The Millers', 'Sean Saves the World', 'Parenthood', & 'The Michael J Fox Show' Adjusted Down". TV by the Numbers. Archived from the original on November 8, 2013. Retrieved November 8, 2013.
Amy and Howard begin collaborating on a neuroprosthetics project, upsetting Sheldon and Raj, who feel they are not spending as much time with them. When they seek solace with an annoyed Bernadette, she exploits the situation to trick Sheldon into doing Howard's chores. Penny successfully employs the approaches recommended in one of Bernadette's parenting books to deal with Sheldon, but Leonard believes she is coddling Sheldon too much. Sheldon and Raj resolve the issue of missing their significant others by spending time together.