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Penny and Sheldon bond during the summer over missing Leonard. Penny calls Leonard, who is partying on the ship and does not sound like he is missing Penny. Penny suggests exchanging secrets with Sheldon, then tells him she appeared topless in an unreleased horror movie. Sheldon says Howard found the clip when they had first met. Sheldon’s "secret" is that he does not like YouTube’s new rating system. Annoyed, Penny decides to leave, but stays and apologizes when she realizes that she hurt Sheldon’s feelings. Leonard shows Penny’s movie to his shipmates.

Leonard surprises Penny by arriving back early and hiding in her apartment. He asks her to keep it a secret from Sheldon, so they can spend some time alone. Sheldon suspects that Penny is cheating on Leonard when he finds clear signs that someone else is in her apartment. Bursting into Penny’s place to catch her in the act, he and Amy find Leonard there. Sheldon gets mad at Leonard for not telling him he is home, and refuses to believe anything he says, although they eventually reconcile with the help of Howard.

After the gang blows off Raj’s murder-mystery party, he creates a scavenger hunt with ten clues that will lead the winner to the location of a gold coin. They first propose making each couple a team, but Leonard suggests "mixing it up" by picking names out of a hat. Penny gets angry and assumes Leonard has proposed this because he did not want to be stuck with her. The teams consist of Sheldon and Penny, Howard and Amy, and Leonard and Bernadette. Both Penny and Sheldon do well figuring out the different clues as they race around Pasadena. Bernadette becomes very competitive, while Leonard is more worried that Penny is mad at him. Amy and Howard, who have not been alone before, bond over their mutual love of Neil Diamond music.

Amy watches Raiders of the Lost Ark with Sheldon. Although she enjoys the film, Amy points out that Indiana Jones is superfluous, since the outcome of the story would have been the same with or without him. After spoiling the movie for Sheldon, he tries to find something that Amy loves and spoil it for her. Sheldon watches Little House on the Prairie, Amy’s favorite TV show, with her and points out historical inaccuracies. Amy, realizing what he is doing, explains that he should just let her know if he is angry, rather than seeking revenge. He does, and Amy apologizes. Penny buys the book The Disappointing Child (in which Leonard’s mother wrote about his childhood problems), for her psychology class, which upsets Leonard. As a result, Penny goes out of her way to make him feel better and Leonard takes advantage of her sympathy. When Howard finds out about this, he tries a similar technique with Bernadette, but it fails. Bernadette tells Penny about Howard’s trick, and Penny, realizing what Leonard has been doing, gets revenge by dressing in a particularly revealing outfit, only to leave a pantsless Leonard talking to his mother on Skype.

Amy tells Sheldon that she will be working on an experiment at Caltech and asks Sheldon how he feels about that. Sheldon has no problem with it, until Howard explains that he would not want to work with Bernadette and have to spend both day and night with her. Sheldon withdraws his approval, though Amy tells him that she is still going to take the job. The next day, Amy is even madder at Sheldon when he embarrasses her at lunch in front of her colleagues. At home, Penny and Leonard try and explain to him that Amy is right. Sheldon then goes to Amy’s apartment and apologizes, but offends her again when he says she can be difficult to put up with. Sheldon mentions Howard’s comments to Bernadette, who then confronts Howard and gets mad after he tries to deny his statements. As a result, Howard is forced to stay at Raj’s place. Later, Bernadette comes over to apologize. Howard promises to spend more time with her, but only after he and Raj finish their video game, enraging Bernadette once again.

Sheldon calculates how to synthesize a new, stable superheavy element, but then realizes that his discovery was due to a mistake, which spoils his achievement, making him feel like a fraud. While his friends, co-workers and the scientific community praise him, Sheldon just wants it to stop. Amy finally tells him he is not deserving of the attention, which Sheldon notes is the most romantic thing Amy could ever tell him. Howard gets everyone to join him in performing a song he wrote for Bernadette, to commemorate the anniversary of their first date. When there is an accident at Bernadette’s lab and she is placed in quarantine, Howard and the gang go to the hospital and sing the song for her. Penny tries to do something romantic for Leonard, after he says that she never does. After failing at finding a romantic thing to do and seeking advice from Raj, Penny tells Leonard that she wishes she could be as romantic as he is. She shows him a box with dozens of mementos – examples of romantic things Leonard has done during their time together. Leonard is shocked, and thinks that the mere fact that Penny has kept all these things is incredibly romantic.

Sheldon, Leonard and Amy run into Dr. Arthur Jeffries (Professor Proton) at the drug store. Leonard gets an e-mail from Arthur asking him to review his recent paper. As Sheldon wonders why he was not asked, Amy points he comes across as annoying. Sheldon goes to apologize to Arthur, only to annoy him more. The next day, Sheldon informs them that his new friend is another famous TV scientist, Bill Nye "the science guy." After Sheldon and Bill leave, Arthur asks Leonard why he puts up with Sheldon. Leonard explains that whilst Sheldon has his quirks, he is the smartest person he knows, and they both need each other. Though Leonard’s answer moves him, Arthur only decides to let Sheldon read his paper after he sees Penny hanging out in the guys’ apartment.

While rummaging through their closet, Leonard finds a DVD rented by Sheldon that should have been returned seven years ago. Leonard desperately asks Sheldon not to flip out, and Sheldon shockingly remains calm and agrees. Sheldon makes Leonard wear an itchy sweater until the DVD issue is resolved, so that Leonard can, metaphorically, walk in Sheldon’s shoes. Leonard searches for the DVD store (that went out of business years ago), then for the owner (who is deceased), then the owner’s next-of-kin (who does not exist), all the while getting a bad rash from the sweater. Sheldon eventually tells Leonard he had discovered the DVD and paid the fine years ago, and that he just wanted him to learn the lesson.

The gang spends Thanksgiving at Mrs. Wolowitz’s house, though she is laid up in bed, so Raj, Bernadette and Amy do the cooking. Penny mentions a Thanksgiving she had in Las Vegas with her ex-boyfriend Zack, joking about how they had a "fake" wedding. Her friends tell her that the wedding was real and that she is legally married, causing tension between her and Leonard. Howard tries in vain to bond with his father-in-law, Mike, who instead starts to bond with Sheldon over football; it turns out that Sheldon has considerable football knowledge, as he was forced to watch the game with his father as a child. After Mike shares beers with Sheldon, they continue to hit it off. After insulting Howard, Amy orders Sheldon to apologize to Howard. A now-drunk Sheldon gestures to Amy and says to Mike, "Ain’t she great?", then swats her on the rear and suggests she get them more beers. Amy is shocked, but delighted at the physical attention. Meanwhile, Penny has invited Zack over to sign the annulment papers to end their marriage (much to the excitement of Raj, Bernadette and Amy). Zack is at first reluctant to sign, saying he is worried about how ending the marriage will affect their non-existent kids. Penny demands that he sign, which he does. Mike finally compliments Howard, but then attributes his kindness to being drunk. Penny and Leonard reconcile.

Sheldon walks out of an interview with Ira Flatow on NPR’s Science Friday after Flatow makes reference to Sheldon’s heavy element discovery being accidental. Amy brings Wil Wheaton to talk about how to deal with unwanted fame with Sheldon. Later, Leonard reveals that he was able to disprove the existence of Sheldon’s heavy element. This infuriates Sheldon, who has now learned to deal with the fame and feels that Leonard took away the one thing that made him famous. Sheldon’s fury peaks when Barry Kripke berates him over Leonard’s findings. Sheldon and Leonard argue with each other on Science Friday, while an embarrassed Amy and Penny listen. While Raj’s apartment building is being fumigated, he and his dog, Cinnamon, move in with Howard and Bernadette for a week. Although Raj is very kind and helpful, his presence highlights the deficiencies in Howard and Bernadette’s relationship, leading them to argue with each other. Eventually, Raj gets thrown out and he moves in with Leonard and Sheldon. Immediately he starts giving Amy and Sheldon relationship advice and, after he tells Amy she needs to be patient with Sheldon’s limits on physical contact, Amy tells him to leave.

Sheldon is in Texas to help with his sister’s home birth, but as usual is totally self-absorbed and unsympathetic to his sister’s discomfort, and no help with anything. In between video calls, his friends wonder what their lives would be like if they never met him. Penny notes that Leonard would be too afraid to have asked her out, Bernadette envisions that she would not have gone out with Howard because of his strange friendship with Raj, and Leonard speculates that Penny would be living with Zack. Amy suggests that Penny would have tried to seduce Sheldon, while Howard notes that he would be caring for his mother even after she was dead (and that he may have even gone crazy and killed her), and Raj and Leonard suggest that as roommates, they would have become obese, due to Raj’s cooking and Leonard’s loneliness. Amy thinks she would have been sad and alone.

Penny is ecstatic when she gets a minor role on NCIS but is devastated when the scene featuring her is cut. As he is comforting her, Leonard accidentally suggests that her scene would not have made a difference to her career, which upsets Penny. She demands that he honestly tell her his opinion on her acting, and he admits that he believes she has unrealistic ambitions for success. Realizing later that his honesty may have hurt Penny, Leonard brings her an offer to audition for a part in the new Star Wars movie by submitting a video. Penny gets drunk and proposes to Leonard after thinking the only good thing in her life is him. Because Penny is upset and drunk, Leonard hesitates in giving an answer; as a result, Penny leaves, thinking that their relationship might be over. After realizing no one finds him funny, Sheldon wants to learn how to become more humorous and attempts to develop a theory of universal humor. In the process, he bores Amy by asking her opinion on which words she thinks are funny. Amy meets up with Howard and Bernadette. Bernadette admits to Howard she often fakes a laugh at his jokes.

Penny quits the Cheesecake Factory to devote all her time to her acting career. Despite saying he supports her, Leonard is not thrilled with her quitting. Meanwhile, Sheldon is forced into taking vacation time, and ends up tagging along with Penny. He says he supports her decision, comparing it to himself devoting all his time to becoming a physicist. Leonard eventually says that even though he could not take a risk like hers, he is proud of Penny for doing so. Bernadette accidentally damages one of Howard’s comic books, and heads to Stuart for help. Stuart does not have the issue, and reluctantly refers her to a rival store. The owner, Jesse, insults Stuart, so Bernadette scolds Jesse and leaves without buying the comic. She later returns to Jesse’s store alone and continues to berate him, but still purchases the comic.

After the guys fail to obtain Comic-Con tickets, Sheldon decides to create his own comic book convention. He decides to ask James Earl Jones, the voice of Darth Vader, to be the celebrity guest at his new event. After finding out where Jones is having dinner, Sheldon approaches him; unlike most of Sheldon’s idols, Jones turns out to be a nice guy who is not turned off by Sheldon’s obsessive personality and hero-worship. Jones takes Sheldon out for a night on the town, going to an ice cream parlor, a carnival, and a strip club, doing karaoke together ("The Lion Sleeps Tonight"), ringing Carrie Fisher’s doorbell and running away, and finally visiting a sauna, where Sheldon begins to get somewhat sick of Jones’s company. After he learns that the guys did not get Comic-Con tickets, Jones invites Sheldon and his friends to be his guests and promises to take Sheldon to Tijuana every night.

Amy plans a romantic Valentine’s Day for her and Sheldon by having dinner with Howard and Bernadette on the Napa Valley Wine Train. Sheldon makes a friend who is as crazy about trains as he is, ruining Amy’s plan. After she confronts him, Sheldon points out that Amy suggested the trip in the first place, prompting her to confess her trick and say that she "deserves romance." Sheldon gets angry and offers her various sarcastic romantic gestures, including drinking wine, staring into each other’s eyes, and kissing; however, the supposedly fake kiss turns into a real one, marking the first time that Sheldon has initiated physical contact between the two. Sheldon even seems to like the intimacy, as he invites Amy to visit the train’s engine room with him.

Leonard and Penny decide to get a dining table for the apartment so that they no longer have to eat round the coffee table. Sheldon objects to the change, blaming Penny who has changed Leonard though Amy has changed Sheldon. Unhappy with this and that Amy told them about the kiss, he decides to break up with Amy. Amy, who has been alerted, agrees with Sheldon to break up, but stops his plan by convincing him that Leonard is manipulating him. Amy is feeding Sheldon his arguments against Leonard, although goes too far when she suggests they move in together. Finally, Amy and Sheldon eat together on the sofa, with the others at the table, until everyone pities Sheldon and they all end up back at the coffee table.

Penny informs the group that she has turned down a role in the sequel to the bad horror movie she was in. Later, Penny’s car engine breaks down leaving her no way to get to auditions, so she decides to get her job back at the Cheesecake Factory. Leonard surprises her with a new car, so she can continue progressing her acting career. After Sheldon insults Howard, Bernadette wants to know why he always insults her husband. Sheldon details a decade of abuse. Howard wants to be a better friend, and invites Sheldon with him on a weekend in Houston where Sheldon can visit NASA and his mother. On the flight, both are frightened by the clear-air turbulence, and each admit that they respect each other as friends and their lives would be empty without each other.

Sheldon and Howard drop in on Sheldon’s mother, but flee after Sheldon sees her having sex. Sheldon returns and gets into an argument, and is sent to his room. After Howard tells him about how he drove away an admirer of his mother, Sheldon apologizes to Mary, saying that he will accept her choices on the outside while condemning her internally for being a hypocrite by going against her religious beliefs. His mother forgives him. The rest of the gang gets roped into a murder mystery dinner arranged by Raj, with Stuart playing the deceased victim. "Traveling" to the future envisioned by Raj, Leonard and Penny broke up because their successful careers. This leads to an argument over the question of what they would do if one of them were required to give up their dream for the other’s success. Stuart tells them that they are the best couple he knows. Penny accidentally reveals she was the murderer, ruining Raj’s game. Leonard suggests no matter what happens they all meet in front of the apartment in 20 years to have dinner together. In the future Stuart is the only one who shows up.

On the subject of decision making, Raj must decide if he is going to date both Emily and Lucy, Penny must decide to accept a role in her horrible horror picture, Serial Apeist 2, and Sheldon is torn between buying a PlayStation 4 or a Xbox One. Sheldon’s decision ramblings really annoy Amy both during their dinner date, where she fakes exaggerated interest, and spending hours at Best Buy contemplating his choices. Leonard and Penny talk to Wil Wheaton who is just depressed about the acting industry. After Penny accepts the job, she finds out that Wil plays the bikini clad orangutan she has to wrestle in the film. Emily tells Raj that she doesn’t mind him dating someone else and he keeps seeing her.

Raj and Howard double-date so that the Wolowitzes can meet Emily before Raj scares her off. At first Raj is afraid that Howard is going to joke about his shortcomings; however, Howard ends up to be the butt of all the jokes. He had been on a blind date with Emily years before, and due to a stomach problem, he severely messed up her bathroom and ran out on her. Howard was given the nickname "Clogzilla". Due to the latest big bang theory discoveries, Sheldon begins to believe he has wasted his life trying to prove string theory. Taking Penny’s advice, he decides to get rid of all his string theory books and move on to a new field of study. As he gets frustrated with all of his possible choices, Sheldon jokes that he might as well take up geology, a subject he believes is not real science. Leonard and Penny tell him not to rush into something. Eventually, Amy puts a drunken Sheldon to bed. When he wakes up, he is horrified to see what he holds in his arms: a book on geology. He also discovers that he made many drunk-calls to Stephen Hawking’s telephone.

After reinstating "Anything Can Happen Thursday", Sheldon, Leonard and Penny wander around town looking for a new restaurant. They find Amy and Bernadette having dinner after lying to their friends. They were tired of hearing Sheldon complain about trying to find a new field to study and Penny’s complaints about her horrible movie. Leonard agrees with them, so Sheldon and Penny storm off. Bernadette admits she lied to Howard as well. Amy tells Leonard she is jealous of how comfortable Sheldon is with Penny. Penny calls Howard and tells him Bernadette lied to him, but Bernadette says she will just put on a Catholic schoolgirl uniform to make it up to him. Raj and Howard watch a horror film to prepare Raj to watch it with Emily. They both find the film disturbing. Emily later says that she too finds the film disturbing, but Raj watches it with her after she says it also turns her on.

The guys prepare for Star Wars Day and plan to watch all six films. Leonard tells Sheldon that Arthur Jeffries (Professor Proton), their childhood hero, has passed away. While Sheldon is sleeping through the film marathon, Jeffries appears to Sheldon dressed as a Jedi Master. He does not know why he is there or what advice to give Sheldon, so he tells him to cherish the people around him before they die. Penny and Leonard attend Jeffries’ funeral, where they start to discuss their regrets in life and Leonard regrets not saying yes to Penny’s marriage proposal. After Leonard returns home, Sheldon wakes up and hugs him, taking Arthur’s advice. Bernadette and Amy make a Death Star cake for the guys while talking about why they became scientists. Finally, Sheldon has another dream where Arthur asks him if watching Star Wars is a useful way to spend his life and Sheldon sees nothing wrong with it.

Howard, Bernadette, and Raj are bringing a treadmill into Howard’s old room in his mother’s house, because of her doctor saying that she needs more exercise. When they reach the top of the stairs, the treadmill slides down the stairs and breaks Howard’s mother’s leg. While Leonard visits the movie set of "Serial Ape-ist 2: Monkey See, Monkey Kill", Penny has a disagreement with the director on doing another take and she and Wil Wheaton are fired. Later, Wil, Penny and Leonard commiserate at a bar until Wil gets a call for an audition for Sharknado 2. Sheldon and Raj go to the movies and they run into Emily who is on a date with another man. Later, Raj and Sheldon discuss why women don’t like Raj. Sheldon suggests that Raj has to get over his fear of being alone. Later, Emily stops by Raj’s apartment. She tells Raj that the guy she was with did her last tattoo and has been asking her out for months, and that she agreed to go to get it over with. Raj feels much better, and they discuss their relationship as well as Emily’s tattoos. Emily then spends the night at Raj’s.

Leonard and Penny tell the group that they are engaged, and while they are happy, everyone makes a bigger deal of Raj and Emily having had sex. Leonard’s mother is unmoved that he is engaged, but accepts Penny because Sheldon is really fond of her. Sheldon is angered the university will not let him change his field of study and considers quitting. He is further upset that Leonard and Penny do not want to live with him after they are married. He is disturbed at Amy’s suggestion they could live together and his last nerve is broken when he discovers that Stuart’s comic book store was destroyed by fire. Sheldon decides to leave town to figure out what he wants. Leonard objects, but Penny says that they should let him go. Sheldon calls Amy to say he is all right, after which a distraught Amy attacks Leonard with a pillow for letting Sheldon go.