The guys return from the North Pole and Penny welcomes Leonard home in style. They are interrupted by a hurt Sheldon who learns that his friends lied to him about his experiment results in order to stop him from annoying them. Sheldon resigns from the university and heads home to Texas. The guys head there and between them and his mother, convince Sheldon to come home. Leonard and Penny finally sleep together but both feel weird afterwards.
Penny and Leonard turn to alcohol to solve their awkward romantic issues. Meanwhile Howard bets Sheldon that he can identify a cricket which has found its way into their apartment.
With Penny in his apartment all the time Sheldon resorts to conditioning techniques to try and modify her behaviour. Howard and Raj dress up and head to a Goth club to try and meet women.
Raj's research runs into a dead end and he fears he will be deported. The only other job he can get is working for Sheldon with inevitable consequences. Howard is now all alone and so tries to spend more time with Penny and Leonard who would rather be alone.
Sheldon has an eidetic memory and it means he doesn’t play games like “Mystic Warlords of Ka’a” because it offers no challenge to him. Raj tries to convince him to sign up for a tournament and only convinces him when they learn that Will Wheaton has also signed up. It seems Sheldon holds a grudge against Wheaton and seeks revenge. Meanwhile Howard recalls a pact which he made with Leonard. They both agreed that should they get a hot girlfriend, they would ask her to set the other up with one of their friends. So reluctantly Penny agrees.
Leonard worries that Penny doesn’t want him to meet her friends. So he asks Sheldon to teach him the rules of football so that he can watch the next game with Penny’s friends. Meanwhile Raj becomes frustrated with Howard’s friendship when he continually abandons him to chase women.
Penny announces that her friend Justin will be sleeping on her couch for the next few weeks. Leonard is upset and they argue so much that Sheldon gets upset. When Howard and Raj argue too Sheldon reveals that it reminds him of his parents arguing. He tries to force Penny and Leonard to make up but when they argue again he runs away to the comic book store.
Leonard, Howard and Raj head to the desert to see a meteor shower. Sheldon and Penny stay behind to work. She dislocates her shoulder and needs Sheldon to take her to the emergency room. Back in the desert the guys unsuspectingly eat some special cookies.
Sheldon is invited to speak about monopoles on NPR. Kripke leaks helium into the room as a prank. Sheldon is upset and Leonard encourages him to seek vengeance. He does but the revenge prank has an unintended consequence. Meanwhile Bernadette wants Howard to commit to a relationship with her. He feels he should be with someone hotter but thinks better of it and tries to woo her.
Bernadette joins the guys for dinner and takes an interest in Leonard’s work. Penny and Howard both feel insecure about this. Penny asks Sheldon to teach her a little physic while Howard confronts Leonard.
Leonard’s mother comes to visit at Christmas time. Leonard hasn’t told her about Penny and she hasn’t told him anything. She has however confided in Sheldon. When Leonard learns of his parents divorce and the death of his old dog he is really upset. Penny takes Beverly out for drinks to get to know her.
Howard and Leonard head out on a double date leaving Raj with Sheldon. Raj bribes Sheldon to come with him to a college mixer and they meet two girls. Meanwhile Penny reveals that she believes in psychics and Leonard laughs at her.
Leonard and Sheldon’s apartment is broken into and all their valuable electronics get stolen. Sheldon feels increasingly insecure and vulnerable. He gets a new security system installed but when he falls victim to it he decides to move to Bozeman, Montana.
Sheldon is stuck on why electrons behave as if they have no mass when moving through a graphene sheet. He tries every way he can imagine to help him figure it out, including working at the Cheesecake Factory.
Leonard is offered a trip to visit the Large Hadron Collider in Switzerland and wants to take Penny as it is Valentines Day. Sheldon of course wants to go and goes to great lengths to change Leonard’s mind.
Sheldon is summoned to court on a traffic violation which he incurred whilst driving Penny to the hospital. The court date is the same day that Stan Lee is coming to the Comic Book Store to do a signing. Sheldon of course gets thrown in jail for contempt while Howard, Raj and Leonard have gelato with Stan Lee. Penny gets Lee's address out of Stuart and takes Sheldon round there to try and make it up to him.
The guys buy a box of random memorabilia and find an actual ring from the movie Lord of the Rings. They each want to do something different with it and end up quarrelling. They decide to each hold onto the ring and the last one to let go will keep it.
Sheldon wins the Chancellor's Award for Science but threatens to decline it when he finds out that he will have to give a speech. It turns out he has stage fright and passes out under the stress. His friends rally around and try to help him. Raj tries to teach him meditation, Penny takes him shopping and Leonard attempts to get to the root of the problem. In the end some alcohol keeps him from fainting.
Leonard tells Penny that he loves her and she doesn't know what to say back. Stuart asks Will Wheaton to join his bowling team in time to take on Sheldon's. Penny leaves during the game though and Sheldon has to hastily organise a rematch. At the rematch Wheaton gets in Penny's ear and makes her wonder whether she should break up with Leonard.
Sheldon and Penny have dinner plans but Sheldon feels very awkward about betraying Leonard. He confesses to Leonard who assures him it's ok. Leonard and Penny begin to discuss Sheldon as if they are a divorced couple and through that find a way to be friends.
Sheldon's female friend Dr Plimpton is coming to stay much to everyone's surprise. She sleeps with Leonard much to Sheldon's disgust and then begins hitting on Raj and Howard.
Leonard asks Penny if he can stay the night with her after a row with Sheldon. He tells her the story of how he moved in with Sheldon and the elevator stopped working.
While bouncing lazers off the moon Penny discovers that her new boyfriend is too dumb for her. She drunkenly blames Leonard and sleeps with him. He is upset when she asks him to forget it happened. Meanwhile Raj and Howard put Sheldon on a dating site and find him a match.
