The university's President Siebert orders the guys to attend a fundraising party. Leonard, Howard and Raj are more than happy to go for the free food and drinks and the promise of a few pretty girls in attendance. Sheldon, however, refuses, believing such fundraising practices demeaning. Amy makes Sheldon reconsider by telling him that his future research funding is dependent upon others, such as Leonard and Raj, making a credible argument to the donors on his behalf. At the party, the guys come across wealthy Mrs. Latham, a formidable older woman who they later learn enjoys making smart people feel ill at ease - which she did with Leonard, Howard and Raj - just for the fun of it. Believing he made a terrible impression, Leonard is surprised to learn that Mrs. Latham wants to speak to him further about his research. But that's not all Mrs. Latham wants from Leonard.

Raj laments the fact of his single status. An admission by Bernadette totally preoccupies Raj's thoughts in his fragile state. Meanwhile, Sheldon has just conducted a guest lecture to the university's brightest doctoral candidates. He believes the lecture was an overwhelming success, but messages posted on various social networking sites show that Sheldon's perception and reality are polar opposites. A less than happy Sheldon decides to take some advice from Amy. As teaching is a performance art, she suggests that he take acting lessons. Despite or in part because he thinks she an acting failure, Sheldon asks Penny to be his teacher, his thoughts along the lines of the old adage, "those who can't do, teach". As Penny and Sheldon go through their antagonistic teacher/student relationship, Penny manages to get through to Sheldon in a way she couldn't have even imagined.

Penny initially declines an invitation from Amy Farrah Fowler, who considers Penny her best friend, to accompany her, Sheldon, Leonard, Howard, Raj and Bernadette to a weekend long science conference at which they'll all be speaking. Penny changes her mind when she learns that the conference is all expenses paid at a four star spa resort in Big Sur. Penny wishes she could change her mind once again when the drive to Big Sur with Leonard, Sheldon and Amy ends up being a nerd's version of a road trip. She probably wouldn't appreciate being in Bernadette, Howard and Raj's car either, the former two who are too happy in love and who demonstrate it in the drive to Big Sur. That love may be in jeopardy when at the conference, Howard meets Bernadette's handsome and 6'7" tall ex-boyfriend Glenn. An unfortunate comment from Howard to Bernadette about her former relationship with Glenn sets off a series of musical beds and musical bedrooms between the seven which culminates in a no holds barred airing of all their feelings at the conference's panel discussion.

Leonard comes up with an idea to develop a smart phone app that would use handwriting recognition software to help in solving their differential equations problems. Although the app's use would be limited to about a hundred people worldwide, he wants to go ahead, and asks Sheldon, Howard and Raj to join him in the project. They all agree. Leonard, as the one who came up with the idea, has a relatively clear vision of how he wants to proceed. However, Sheldon believes his way is best and wants to be among things CEO and CFO of the project, and to have it named after him. When Sheldon's controlling ways become too much for Leonard to handle, Leonard fires him from the project team. Sheldon tries whatever he can to make life difficult for the other three to complete the project, and even believes he may have lost Leonard as a friend for good. Penny takes pity on a moping Sheldon, but comes to regret it. She has to figure out a way to foist Sheldon back onto Leonard.

Penny starts dating Zack again. Used to being the target of bullying, Leonard, Sheldon, Howard and Raj instead bully Zack through their implications to him that he's stupid. Not fully realizing what they're doing until Penny points it out to them, the guys decide to apologize to Zack in the only way they can. Accepting their apology, Zack decides to start hanging out with them, much to Penny's chagrin. This hanging out leads to the idea that Zack should replace Leonard as Superman in their group Justice League of America costume for the New Year's Eve party at the comic book store, with Penny the sixth wheel as Wonder Woman. These actions lead to questions from Leonard to Penny about why she's back together with Zack.

Amy experiences strange symptoms, which she believes are signs of a flu. They include an elevated heart rate, sweaty palms, dry mouth, and localized vascular throbbing. As Penny and Bernadette were present when the symptoms began, they know that Amy doesn't have the flu: she is in lust with Penny's ex-boyfriend, Zack Johnson. As Amy and Sheldon finally come to the conclusion that Amy is feeling womanly urges for the first time in her life, Sheldon has to come to terms with what his feelings for Amy are. They also have to decide how best to satisfy Amy's new biological urges. Meanwhile, Howard and Raj get into an argument: if they were to acquire super powers, who would be the superhero and who would be the sidekick. They have to come up with a way to settle the argument.

Penny's father, Wyatt, is in Pasadena for a visit. Leonard learns that Penny told her father that she and Leonard got back together again, as Leonard is the one and only of her boyfriends of who he has ever approved. Leonard agrees to go along with the ruse, but much against Penny's chagrin, he does so on his terms and not hers. But what would happen if Wyatt found out the truth? Sheldon, believing that Leonard and Penny have indeed gotten back together, decides to amend their roommate agreement to compensate for the Penny factor. Meanwhile, Raj has finally been allocated time to monitor a high powered telescope for twelve hours, and he invites Howard along, who in turn invites Bernadette. Raj is initially peeved at Bernadette's presence since he doesn't feel like he can drink (to be able to speak to her) and monitor the telescope at the same time. Raj makes the decision to consume alcohol, and his arc of drunkenness over the course of the evening ends with a close encounter with Howard.

Leonard, Sheldon, Howard, Raj and Amy are planning to go a see a special screening of Raiders of the Lost Ark (1981) with 21-seconds of previously unseen footage which, from what Leonard hears, solves some major controversies about the 21-second shorter version. Penny - after just having watched the movie for the first time in her life - has no interest in seeing it again with the 21-seconds, so she and Bernadette decide to have a girls night. Since she's a girl, Amy decides to crash the girls' party instead of going with the guys, which places the girls night in a whole different dimension, until they decide to play Truth or Dare. Meanwhile, Sheldon wants to leave to get to the cinema at five o'clock for the midnight screening, instead of having a leisurely dinner beforehand at the Cheesecake Factory. When they arrive at the cinema when Leonard, Howard and Raj want to get there, Sheldon gives them a big "I told you so" when they find the line-up is enormous. Sheldon does whatever he can to see the movie or else. His goal is even more focused when his arch nemesis Wil Wheaton receives special treatment to get into the screening.

Howard has been chosen to work on the Defense Department's Laser Equip Surveillance Satellite project. He needs security clearance to work on the project which means the FBI will be interviewing each of Sheldon, Leonard and Raj, with the interviews being conducted by Agent Page, a beautiful young woman. Raj can't speak to her until he gets drunk, and still then he believes her sole goal is to deport him back to India. Woman-hungry Leonard decides to try his new confident persona to pick her up, which has unintended consequences. And Sheldon wants to speak more about his past encounters with the FBI than about Howard. Howard fails to receive the clearance to work on the project due to one specific incident in one of the three interviews. The guilty party fails to disclose the gaffe to Howard. Will the guilty party ultimately confess and will he be able to make it up to Howard regardless of if that confession happens?