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..."
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.
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.
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 needs half a billion dollars to prove his latest concept of string theory, which the University cannot afford to fund. Crowdfunding and selling some of his most valuable comic books to Stuart give him a small start. When Raj mentions gambling in Las Vegas, Sheldon goes there but is caught calculating odds by security before he can make any bets. Meanwhile, Amy takes Penny and Bernadette shopping for her wedding dress. She loves an old-fashioned one that the other girls admit that they find ugly, though Penny assures Amy she can make her own decisions about her wedding. Sheldon, however, comes home and sees Amy in the dress and loves how she looks.
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.
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.
Bernadette's due date arrives but she still hasn't given birth. As Amy and Howard work together at the college, the rest of the friends try various ways to initiate her labor, though Sheldon wants to play a complicated board game instead. Amy shocks Howard by saying Bernadette has already decided to name the baby after her father, Michael. He doesn't agree and everyone makes suggestions as to what to name the baby. Bernadette goes into labor and gives birth to a son named Neil, after Neil Armstrong, Neil Gaiman, and Neil Diamond, with Michael as the middle name. At the last minute, Howard relents to name him Michael as Bernadette got six stitches.
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 is still despondent over the disproving of his and Amy's theory on asymmetry. Leonard brings out a VHS tape of a pep talk that Sheldon recorded as a boy, but it turns out that his father had recorded a long-ago football game over it. Sheldon, however, is buoyed by a halftime pep talk his father gave the team, realizing he and his father had more in common than he previously thought. This causes Amy to view asymmetry and symmetry in another manner and they decide their theory may not be dead after all. Bernadette finds an old tape of Howard preparing to audition for The Magic Castle. She insists he fulfill his dream and audition with her as a coach, drawing on her beauty pageant experience. Howard eventually decides to audition his own way, and promptly botches his chances by accidentally destroying a judge's Rolex.
I agree with Jeff. The finale was hardly “perfect”. I thought they took the safest route possible; and there were only a few good laughs. Some of it was predictable; winning the Nobel and fixing the elevator. The prize ceremony wasn’t even particularly interesting. Having each friend stand and be recognized at a Nobel ceremony seemed way of place…even for Sheldon. The writers were obviously struggling this last season for new material , and the finale was no exception. I still think Raj should have ended up with ‘someone’, as they felt the need to pair everyone else off during the series. (Even Stuart got a girl.). All in all, I found the finale wanting. I thought going in that I might burn it to DVD as an episode to keep to watch again. I’ll pass.
When Raj misses out on a job at the planetarium, his father says he has no confidence because Howard always makes fun of him. Raj distances himself from Howard and later gets the job. Howard is hurt by this (even after apologizing to him) and tries to make amends with Raj after his first performance at the planetarium but, when he sees him get a date, he leaves without speaking to him, thinking that the latter's life is better without him. Meanwhile, Sheldon and Amy try randomly dividing up wedding tasks, but they keep arguing. The only thing they can agree on is to get married, so they decide to just get married at City Hall. However, Sheldon decides that he wants a first dance with his new wife and they go home to plan their wedding.