- Leonard's book raises questions, and Amy guest stars on the new Professor Proton show.
- The reboot of the "Professor Proton" show with Wil Wheaton assuming the titular role from the now-deceased Arthur Jeffries has just started airing. Sheldon wanting to be Professor Proton has placed Wil back on his enemy list. Without watching it, Sheldon decides to do whatever he can to ensure that the show doesn't succeed. However, in Amy convincing Sheldon at least to watch the show before he criticizes it, Sheldon is surprised that he actually does like the show. But a specific incident on the show brings to light something within Sheldon about which he was somewhat unaware that negatively affects his relationships with his friends, including Amy. Will that incident lead to Sheldon becoming a more empathetic friend, especially to Amy? Meanwhile, Leonard has just started to write his novel, the central character, he wishfully basing on himself, being a physicist named Logan Dean who solves crimes using science. Bernadette, who reads the early pages, convinces Leonard that the lead female character, Ilsa, a beautiful, tough, mean blonde, is based on Penny, whether it be consciously or unconsciously done. If Penny finds out, she may not take too kindly to that characterization of her. If Leonard didn't consciously base it on her, could Ilsa actually be someone else?—Huggo
- Sheldon and Amy are supposed to go to Leonard and Penny's apartment to watch the new Professor Proton show. Sheldon refuses to go since he doesn't want to watch his sworn nemesis, Wil Wheaton, as Professor Proton. Sheldon is planning on complaining about it without ever watching it. Amy suggests that they watch it together so he can find specific points to criticize. While watching the show, Sheldon gets excited when Wil describes how they are going to build a hovercraft out of some common household items.
Penny enters her apartment to find Leonard clattering away at a his computer which is making typewriter sounds. He is working hard on his mystery novel, writing the scene where his protagonist, Logan Dean, arrives at the CERN Collider in Switzerland.
Back in apartment 4B, Sheldon and Amy are having fun with their toy hovercraft. Then on the show Professor Proton tells his science joke of the day and he introduces a real astronaut as his surprise guest: Howard Wolowitz. Sheldon is upset that Wil didn't ask him to guest-star. Amy reminds him that he recently spearheaded an Internet petition to get Wil fired.
During lunch at work, Leonard is describing his novel where his hero discovers a new atomic particle, the Gluino, AND a murder. Howard suggests that he talk to Bernadette, since she had been watching lots of detective shows while confined to bed. Howard tells Sheldon that he should apologize to Wil to be invited to his show
Bernadette is enjoying Leonard's mystery novel and tells him she has no idea who the murderer is. Neither does Leonard. Bernadette then asks if Penny knows that one of his characters is based on her: Ilsa, the head of the institute who is "a confident, ball-busting beauty that keeps rolling her eyes" at the hero.
A scene from the novel is shown: A group of professionals are in a laboratory at the CERN Swiss facility. Logan looks at Ilsa and intones, "It's murder." Ilsa replied, "Figure that out yourself, genius?" Logan replied, "Okay, no need to be snarky." Ilsa looks at him suspiciously, "Who would want to kill him?" Logan looks around the room. "Could be anyone. Dr. Silvers. [Howard look-alike] Dr. Prakash. (Raj with a goatee) Hans the janitor. (Stuart with a big mustache) But the door is locked, so it has to be someone in this room." "Wow, you are on fire," snaps Ilsa, walking away.
Wil Wheaton answers his front door to find Howard, who apologizes for having brought over Sheldon. Sheldon tells Wil that he is no longer on his enemies list. Howard gets Sheldon to say he was sorry and that he genuinely enjoyed his show and wants to be invited to it. Wil instead asks if Amy would be interested in being a special guest on Professor Proton, since he wants to promote women scientists. Sheldon proposes that he and Amy both be on the show.
Back at home, Penny tells a nervous Leonard that she finds the Ilsa character kind of mean much like Bernadette whom she is sure that Ilsa was based on.
Novel: Logan tells everyone, "But the door is locked, so it has to be someone in this room." "Wow, you are on fire," snaps Ilsa walking away. [Bernadette] Logan continues with his analysis. "Each one of you had a motive." "I think you're neglecting your own motive, a massive inferiority complex," snaps back Ilsa. "It's not massive. Just average size," replies Logan less confidently. Hans the janitor breaks in, "I don't mean to interrupt, but somebody's tracking blood everywhere so - never mind, it's me." Logan: "I have an alibi." Ilsa snaps at him, "Yeah, he's not smart enough to pull off a murder like this."
Back: Leonard claims that Ilsa wears glasses like Bernadette even though it doesn't say that in his novel. Leonard walks off trying to convince her that the mean boss is Bernadette.
Amy is working on her computer when Sheldon returns and asks if she would like to be on television on the Professor Proton show. Sheldon felt that she would want to promote science for little girls, she doesn't want to upset Sheldon (due to his feud with Wil), who finds that situation very upsetting.
Penny is sitting on Bernadette's bed hanging out because Leonard is working late. Penny wonders if the Ilsa character bothered her. Bernie then mentions that Leonard said that it was based on Penny.
In the Caltech cafeteria, Sheldon starts talking about the distressing news how Amy doesn't do things so that he won't get upset. Howard tells him that everybody does that all the time. He doesn't want to have that kind of relationship with Amy. Sheldon insists that he is going to change.
Penny is reading the book trying to determine if the Ilsa character was her. Novel: Logan is lying against a desk wounded. Ilsa observes, "It looks like the bullet went straight through you. Damn it, Logan. When are you gonna stop?" Logan replies, "I didn't get my PhD in quitting." "He's losing a lot of blood," remarks Dr. Silver. Dr. Silver pleads, "We've got to find some bandages." Ilsa shouts, "No. There's no time," as she tears off her sleeve placing the cloth on Logan's shoulder. "Does it hurt?" "Everything you do hurts," Logan replies. "Then why do you keep coming back for more?" she asks.
Back: Leonard returns. Penny is angry because she thinks that Leonard feels that she is mean and that everything she does hurts him.
In 4B, Sheldon and Amy are playing chess and Sheldon lets her win. Amy wants to know what is going on. Sheldon says that he is responding with humility and admiration. He wants her to be able to do things she wants to do without having to consider upsetting him.
Now Leonard is talking to his mother that he might be subconsciously writing about Penny. Beverly corrects him and wishes that she didn't have to do it all the time.
Novel: Ilsa leans over the wounded Logan. [Beverly] "You're a physicist. What makes you think you can solve a crime," asks Ilsa.
Back: Leonard leaves his mother as she again corrects his grammar. He runs over to Penny to tell her that she was writing about his mother, not his wife. Penny then imagines the story.
Novel: "I think you're neglecting your own motive, a massive inferiority complex," snaps back Ilsa. [Beverly] "It's not massive. Just average size," replies Logan less confidently... [Later] Dr. Silver pleads, "We've got to find some bandages." Ilsa [Beverly] shouts, "No. There's no time," as she tears off her sleeve placing the cloth on Logan's shoulder. "Does it hurt?" "Everything you do hurts," Logan replies. "Then why do you keep coming back for more?" she asks.
Back: Penny is looking weird with that dialog between Leonard and his mother. Leonard then storms out wondering why he was even writing a book since he was a physicist.
Sheldon and Amy are watching the conclusion of Professor Proton with Amy appearing on it. Wil says that it was a pleasure to have her on. Sheldon tells her how proud he was; while she can tell how hard he was trying to hold it in. Amy heads off to bed so Sheldon can go up on the roof and scream at the top of his lungs.
Title reference: The uncertainty of on which woman in Leonard's life he subconsciously based the mean boss character in his novel.
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