Leonard and Sheldon are brilliant physicists, the kind of "beautiful minds" that understand how the universe works. But none of that genius helps them interact with people, especially women. All this begins to change when a free-spirited beauty named Penny moves in next door. Sheldon, Leonard's roommate, is quite content spending his nights playing Klingon Boggle with their socially dysfunctional friends, fellow Caltech scientists Wolowitz and Koothrappali. However, Leonard sees in Penny a whole new universe of possibilities ... including love.
Raj and Howard sign Sheldon up for online dating and find his female version for him.
Penny shows up at Leonard's door, drunk and lonely, and takes him straight into the bedroom. Leonard wakes up the next morning overjoyed until he finds out that Penny regrets the drunken encounter.
Leonard lands up at the home of Leslie Winkle and attempts to have casual sex with her. She shuts the door on his face.
Penny asks Sheldon, Leonard and the guys how they all met. Leonard narrates the story of how he met Sheldon and later Howard and Raj too joined them.
Sheldon meets a famous female physicist online, and invites her to come visit and stay at his apartment. Leonard realizes that it is the famous and very attractive female physicist that he has a big thing for. The woman pays him a visit to his room in the middle of the night. Penny gets mad at this and Sheldon feels betrayed because Leonard is "playing with HIS friend." The woman turns out to be a bit of a hussy, and proposes a foursome. The boys back out.
Sheldon tries to hide from Leonard that he is still "seeing" Penny. He expresses to Penny that he wants to remain friends. In order to not ruin it with Leonard, he has dinner with the guys and then sneaks over to Penny's for dinner. Finally, Sheldon breaks down and tells Leonard that he is still "seeing” Penny. Leonard does not mind. At the end, they agree that they can be friends.
Leonard tells Penny he loves her but she replies with "thank you". She says she committed to early in the relationship and the outcome wasn't good so she didn't want to rush into it and ruin what they have.
Sheldon, Penny and the guys meet up with Stuart's team at the bowling alley. Stuart has a surprise replacement for a regular teammate - Wil Wheaton. Sheldon seeks to take revenge but Leonard and Penny get into an argument and storm off. He convinces them back but Wil plays dirty tricks and the two storm of again. Sheldon vows revenge some other time.
Sheldon gets stage fright on learning that he was to be honored with a prestigious award by the University. Penny tries to give him confidence and takes him to buy a professional suit, while Leonard and Koothrappali try to provide psychological and spiritual guidance. On the night of the event, Sheldon initially appears composed but soon gets nervous until Penny gives him lots of alcohol to stand through the evening.
In a parody of "The Lord of the Rings," the guys fight over a ring they believe was an original prop from the movie. Leonard wants to give the ring back to its original owner. Koothrappali wants to sell it so that he can get a jet ski. Sheldon wants to keep it with him. Sheldon sneaks into Penny and Leonard's room in the middle of the night to steal the ring off of Penny's neck where she is wearing it to keep it safe. Leonard makes everyone believe that he has sent the ring back to New Zealand to the original owner but has really hidden it in his room.
Sheldon misses out on an opportunity to meet Stan Lee, creator of Spiderman, at the comic book store as he is summoned to traffic court. Sheldon insults the judge and ends up in jail for contempt.
Penny feels horrible for being responsible and goes to the comic book store to ask Stuart for Stan Lee's phone number. Stuart is so smitten with Penny, that he actually gives her Stan Lee's home address. Penny takes Sheldon to Stan Lee's house but Stan Lee has Sheldon arrested...again.
Leonard is invited to Switzerland on Valentine's Day to see the CERN Supercollider, the world's largest and highest-energy particle accelerator. Sheldon is shocked when Leonard decides to take Penny, making it a romantic Valentine's Day present, instead of him.
Penny gets sick the night before they have to leave so Leonard decides to make peace and invite Sheldon who is also horribly sick. Penny and Sheldon end up staying home and Leonard is forced to take Koothrappali to Switzerland.
Sheldon cure of "Theorist's block" is a broken dish at the Cheesecake Factory where he just starts working without being hired.
Sheldon and Leonard's apartment is broken into so installs a home security system that goes all wrong and ends up ensnaring Penny in a net. Sheldon is so nervous about another break in he insists on sleeping in their room with them.
In the end, he decides to move to Bozeman, the safest city in the country. Unfortunately, when he arrives, he is immediately robbed at the train station, so he buys a one-way ticket back to Pasadena.
Penny and Leonard get into an argument over Penny visiting a psychic. Later, Leonard ends up apologizing and agrees to meet Penny's psychic. Raj and Sheldon meet two cute girls and one of the girls really likes Sheldon. They all go back to Sheldon and Leonard's apartment, and as Raj gets cozy with one of the girls, the other girl, Martha, suggests to Sheldon that she "tuck him in." This goes right over Sheldon's head and he totally rejects her advances and just replies, "Oh thanks, but the only person who tucks me in is my mother."
Leonard's mother Beverly returns for a visit and informs him that she and his father are getting a divorce after she discovered he cheated on her.
Penny decides to catch up with Beverly and at the bar tells her about her relationship with Leonard. Beverly and Leonard come to a new understanding about how they need to include one another in their lives more. Penny is thrilled that Beverly finally thinks she is adorable.
Penny feels she knows little about science talk now that Bernadette is part of the gang and asks enlists Sheldon to teach her about physics.
Wolowitz gets jealous when Bernadette shows interest in Leonard's work but she gives him a piece of her mind when she comes to know of this.
Penny rattles off a monologue about what Leonard is working on.
Wolowitz first pulls away from committing to Bernadette and then goes overboard and proposes her. He proceeds to sit down at a piano and sings Bernadette an apology to tune of the Four Tops song "Bernadette". While Penny is horrified, Bernadette thinks it is sweet.
Kripke plays a prank on Sheldon during his interview with Ira Flatow. Sheldon returns his prank but unfortunately for Sheldon, the President of the university and the board members are caught in the mix.
Leonard, Koothrappali and Wolowitz head to the desert to see the Leonids meteor shower. Wolowitz starts hitting on a few girls who give him cookies to get him away. The guys eat the cookies and get high after which Wolowitz reveals how he lost his virginity to his second cousin. The guys end up forgetting all about the meteor shower.
Penny falls in the shower and Sheldon comes to her aide and ends up seeing her naked. He takes her to the hospital and cares for her.
Penny and Leonard have a huge fight after Penny tells him that a male musician friend of hers, who she dated for a short time, is coming to stay with her while he is in town. Koothrappali and Wolowitz then take sides and begin to argue about who is right in the fight between Penny and Leonard.
Sheldon can't handle fights so he takes refuge in the comic book store. Penny and Leonard have a hard time convincing him to come out.
Sheldon takes over as the hit of the football watching party that Penny hosts leaving Leonard who invited Sheldon angry and upset.
Koothrappali wants Sheldon to be his partner in a card tournament. Sheldon at first refuses as he was let down by Wil Wheaton as a child. Sheldon meets Wil in the finals and buys his sob story that he did not turn up for an event that Sheldon had looked forward to as a child as his grandmother passed away. Sheldon gets emotional and throws the match letting Wil win. It turns out Wil gave a fake sad story.
Wolowitz reminds Leonard that as per a pact they once made if any of them every managed to get a hot girlfriend, she would to have hook up the guys with her hot friends. Penny reluctantly agrees and they all go out on what turns out to be horrible date. But they bond in the end telling each other stories of their mutual hatred for their mothers.
Koothrappali reveals that he will soon be deported since the university will no longer fund his research and he is here on a work visa.
Wolowitz tries to find Koothrappali a new job but Koothrappali hits on a beautiful, new female scientist at the interview and blows it up.
Sheldon offers Koothrappali a job but Koothrappali question Sheldon's research methods after which he gets fired.
Wolowitz meets a Goth girl online and goes for a tattoo with her but chickens out when the time comes.
Sheldon tries to use positive reinforcement to train Penny. Leonard catches on and initially is appalled but later decides to use it on Penny to achieve his own objectives. Penny gives Leonard a little negative reinforcement after she figures out.
Penny feels awful when she learns from Sheldon that Leonard thought sex with her was not all it was cracked up to be. Penny and Leonard decide to have a drink and loosen up a little bit. They get a bit too loose, and end up getting sick, leaving their new intimate relationship in an even weirder place.
The guys alter Sheldon's research to put him in a better mood for the duration of the trip to North Pole. Sheldon is humiliated, resigns from the university and runs back home to Texas and his mother.
Penny is so excited to see Leonard back from the trip that she immediately drags him into her apartment and kisses him.