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.
Kevin Sussman as Stuart Bloom (recurring seasons 2–5, 7, starring seasons 6, 8–12): A mild-mannered, under-confident owner of a comic book store. A competent artist, Stuart is a graduate of the prestigious Rhode Island School of Design, and though he is socially awkward he possesses slightly better social skills. Stuart implies he is in financial trouble and that the comic book store now also is his home. He is later invited to join the guys' group while Howard is in space. Stuart gets a new job caring for Howard's mother later. After Mrs. Wolowitz's death, Stuart continues to live in her home, along with Howard and Bernadette, until he finds a place of his own.
Penny runs into her ex-boyfriend Zack, who has gotten rich from selling his company and married a similarly dim-witted woman named Marissa. Meeting with Leonard and Penny, they say Zack is infertile and ask to pay Leonard as a sperm donor so they can have a baby. Leonard is flattered, but Penny finds it creepy. Leonard says that since Penny decided she did not want to have children, he should be allowed to help another couple with this issue. Sheldon advises him to think about the emotional toll this could have on him. Leonard says he will not do it if Penny objects; Penny says she will support whatever decision Leonard makes. Meanwhile, Raj tries to get Anu back but she points out he just wanted to be married like his friends. Raj points out that Anu is similarly looking for a quick marriage. He admits to Anu that he really likes her and they decide to start their relationship as just dating.
"The Skank Reflex Analysis" "The Infestation Hypothesis" "The Wiggly Finger Catalyst" "The Russian Rocket Reaction" "The Rhinitis Revelation" "The Good Guy Fluctuation" "The Isolation Permutation" "The Flaming Spittoon Acquisition" "The Shiny Trinket Maneuver" "The Recombination Hypothesis" "The Beta Test Initiation" "The Werewolf Transformation" "The Hawking Excitation" "The Stag Convergence" "The Countdown Reflection"
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.
Initial reception for the series was mixed. The review aggregation website Rotten Tomatoes reported a 52% approval rating for the first season based on reviews from 23 critics, with an average rating of 5.18/10. The website's critical consensus reads, "The Big Bang Theory brings a new class of character to mainstream television, but much of the comedy feels formulaic and stiff." On Metacritic, the season holds a score of 57 out of 100, based on reviews from 23 critics, indicating "mixed or average reviews". Later seasons received more acclaim and in 2013, TV Guide ranked the series #52 on its list of the 60 Best Series of All Time.
Leonard tells Zack and Marissa he will father their child, but Penny tries to seduce him despite knowing he has to be abstinent for a few days. Her visiting father, Wyatt, points out her actions suggest she is more conflicted over having kids than she lets on, which she admits. Wyatt says he will support her no matter what. Meanwhile, Sheldon and Amy warn that he will not be allowed to raise a child that is not his. Leonard decides not to go through with it; he tells Zack to have Sheldon be the donor, but Amy forbids it. Meanwhile, Howard turns Raj's cancelled bachelor party into a couples' trip into a zero-gravity aircraft, though he's convinced that Bernadette would hate it. Bernadette tries to get out of it so Howard sits out, forcing Bernadette to go through with it just to prove him wrong, though she does not enjoy it.
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.