Penny and Sheldon bond further over missing Leonard, though Sheldon doesn't admit that he misses him. Howard tries to help Raj get over Lucy. Amy and Bernadette are away together at a convention and do their own bonding.
Leonard and Sheldon are on the phone, while Leonard is still on the research boat from last season. As the research team is in some rough seas, Leonard tells Sheldon that he is going back inside. But then Sheldon hears a haunted roar. Sheldon remarks that over the terrible phone connection, it sounded like someone had released a kraken. Leonard disagrees saying that there is no such thing as a kraken, when a giant tentacle reaches over the side of the ship, picks him up and drags him into the raging sea. Sheldon wakes up in his own bed, screaming, since he is having a nightmare. He runs over to apartment 4B.
"(knock..knock..knock) Penny. (knock..knock..knock) Penny. (knock..knock..knock) Penny."
Penny opens the door and asks him: "What's the matter?" without any anger whatsoever. Sheldon replies that he is concerned that she might be missing Leonard, resulting in her having bad dreams, like the kind you would get, if you watched Clash of the Titans right before you went to bed. He mentioned that in the dream, Leonard had switched the Back To The Future DVD's around. Penny says good-night, however Sheldon suggests that he should sleep in her place, so that she will not miss Leonard as much. Penny agrees that that would make her feel better to appease him. Sheldon walks passed her to her bedroom, says goodnight and closes her door. She no longer even flinches at his actions, smiles, shakes her head, and closes her apartment door, indicating that their relationship has changed quite a bit.
Raj, Sheldon, and Howard are having breakfast in the cafeteria. Raj is heartbroken about losing Lucy and compares her to a grease stain he saw in the parking lot. Sheldon tells Raj, the astronomer, to get his eyes back on the stars like the Dung Beetle. Raj asks if that is true, while Sheldon counters that everything he says is true. Howard tries to cheer Raj up by pointing out that since he can now talk to women, he can meet someone else. After Raj tells Howard, that he sees Lucy's smile in his chicken potpie, Howard chops off the crust, destroying the illusion, and making him stop. Howard suggests that Raj attends the social for welcoming new post-doctorates, to meet some women. Howard agrees to go with him, because he wants him to be happy. Sheldon isn't coming, because even though he wants Raj to be happy, it isn't enough for him to want to help him.
Amy and Bernadette are attending a convention, and saying good night to their guys. Bernadette tells Howard that she loves him and really misses him. Amy must convince Sheldon that she won't bring back any bedbugs because she did check the bed, and further refuses Sheldon's request to make her sleep in her garment bag.
The next night, Penny and Sheldon are hanging out in apartment 4A. Sheldon asks Penny if she ever wondered if Starfleet Captains... to which she immediately cuts him off with a "No" while she flips through a magazine. Sheldon then welcomes her to the world of Star Trek 3D chess. Penny remarks that he should admit that he only wants to play that game because he misses Leonard. Sheldon replies that she overestimates the significance of Leonard in his life and gives some examples of things he doesn't miss. Penny then calls him an emotionless robot. Sheldon says: "Well, I try", Penny says she just wants to get the game over with. He then wants to know if she would help him with his zipper; one of the things he claimed not to miss about Leonard.
Raj and Howard are at the post-doctorate social. Raj meets one boring female grad student who is talking about her thesis. When Howard asks how it went, Raj answers: "If you like dry factual statements interspersed with painful moments of silence, it went bananas." Howard then notices Mrs.Janine Davis from the Human Resources Department whose husband has just left her for a young, gorgeous undergraduate student. She approaches and greets them. Raj brings up the subject of infidelity among penguins. He tells her not to feel unattractive since her husband left her, because it happens among penguins and they are adorable. Mrs. Davis looks at him and walks away. Howard comments: "It was better when you couldn't talk to women."Amy and Bernadette are lounging in the hotel bar looking over the schedule for the convention events. Commenting on a seminar, Amy says that brain lesions are fascinating, unless they are yours, then they are a drag. Bernadette then toasts to the advancement of science to which Amy adds to the sick and dying who make it possible. They find it nice to talk shop for once, since all they talk about around Penny is boys. The waiter brings over two drinks from a pair of gentlemen at the bar, which gets Amy very excited. Amy waves to the fellows, while Bernadette tells her to be cool. Amy says: "Guys are hitting on us, and not just to get to Penny." Bernadette agrees, and shouts out a cheery "Thank you" to the gentlemen.
Penny makes a move in their chess game. Sheldon comments that it is a bad move, since his queen can take her rook from below. Penny gets excited that the game is over. Sheldon doesn't make the winning move because, according to him, they are having too much fun. Penny stands up and wants to take a break. Sheldon tells her that they are all out of alcohol. Penny denies that she wanted a drink, moans and then sits back down. Penny wonders what Leonard is doing, and that she misses him so much. Sheldon suggests that: "We could call him! I-I mean you can call him." Sheldon makes it clears that the absence of his friends does not cause him pain, and that like rock and roll bad boy Paul Simon once said: "I am a rock, an i...i...i...island." Penny decides to call Leonard, which makes Sheldon highly excited, and he pleads with her to put him on speaker phone.
Leonard, now sporting a beard, is dancing in a room full of fellow scientists having a party. His phone rings, and he tells the woman next to him that his pants are buzzing. Penny tells Leonard that it is Penny, and he gets the whole room to shout "Hi, Penny!" Penny says that it sounds like he is having a good time. Leonard shouts back that he is having the best time of his life. Sheldon asks: "Isn't it 5:30 in the morning there?" Leonard tells his colleagues the time and they all cheer. Penny explains that they were missing him. Someone on the ship yells out "iceberg". This comment worries Sheldon. However, Leonard tells him that it's just part of a drinking game and everyone has to take a shot. After the connection goes dead, a peeved Penny says: "I cannot believe we were missing that jerk." Sheldon: "you were."Bernadette returns to their table in the lounge, after telling the guys that bought them drinks that they were both unavailable. Amy then concludes that she can drink the free drink without "having to give up the goodies". Bernadette agrees and then comments to Amy that no one would blame her if she takes it further. Amy asks Bernadette why no-one would blame her, and that it sounds like Bernadette meant that Amy could do better than Sheldon. Bernadette avoids answering by remarking how strong their drinks are, but Amy wants her to explain herself. Bernadette tells Amy that she isn't married and that her boyfriend in kind of "Sheldon" to which Amy counters back that Bernadette's husband is extremely "Howard", and what the point with this statement is. Bernadette replies that what she said was stupid, and that she wants to forget it and go back to having a nice time. Amy answers: "We could, but unfortunately my brain is lesion-free, and I remember that rotten thing you just said about my Sweet Baboo." Bernadette then apologizes and asks if they can just let the subject go. Amy says, "Sure." As Amy takes another sip of her drink, she says that Bernadette's husband is weird and his clothes are ridiculous.
Penny is upset. She can't believe that she has been sitting around missing Leonard. She asks Sheldon if he knows what the worst part of the situation is and he replies that she has to deal with it without vodka. Penny gives a definite "no" and then retreats to "yea". Her second worst part is that he doesn't appear to be missing her at all. Sheldon comforts her with the fact that she still has her health. Penny asks him if that is supposed to be comforting. Sheldon then replies that in a hundred years they'll both be dead and it won't matter. Penny insists that he should be saying that the only reason he is partying is to cover up the pain of missing her. Sheldon disagrees and doesn't think that that is true. Penny wonders why she is upset at all. Sheldon then thinks that she might be worried that he is having drunken coitus with another woman. Penny tells him to stop trying to make her feel better. Sheldon says that he can't because Leonard made him promise to take care of her. Penny calls Leonard's action sweet and it changes her mood. Sheldon also gets a sailor hat when Leonard returns if he does a good job. Penny now misses him even more. Uncharacteristically, Sheldon replies with he feels that Leonard is tormented every minute he is away from her loving embraces and sweet cherry lips.
Back at work Raj approaches Janine Davis in the cafeteria to apologize for hurting her feelings and insulting penguins. He then tells her that they both are experiencing the throws of heartbreak and that he is going to tell her about his.
Sheldon has made Penny a hot beverage to comfort her contained in a "to go" cup which includes a veiled hint. Penny says that it's early and still wants to do something. Sheldon has been toying around with the idea of 4-D chess. Penny just wants to talk, but stops Sheldon when he starts to describe 4-D chess. Penny asks him to tell her something about him that she doesn't know. Sheldon says that owns nine pairs of pants. Penny asks for something a little more personal. Sheldon says that he owns nine pairs of underpants. Penny decides to take a turn and tells him that when she first came to California she made a low budget movie about a killer gorilla in which she did a topless scene. She was so ashamed and glad that the movie was never released. Sheldon says that he's seen it, "Serial Apeist" which shocks Penny. Howard found the movie online the day they first met Penny. Sheldon then says that he sees what kind of personal revelations she is talking about. He says that he doesn't like the new YouTube rating system. He feels ten pounds lighter after getting that off his chest. Penny gives up and decides to go to bed. Then Sheldon tells her another thing she doesn't know, that she just hurt his feelings. He opened up to her about something very upsetting and she treats it like it's nothing. Penny tells him that she is sorry and that she should have known better. She offers a hug and he puts out his hand for a hearty handshake. Penny ignores him and hugs him anyway. He puts one hand on her back in return and tells her that he now knows how she felt when she was mauled by that sex crazed gorilla.
Bernadette and Amy are getting ready for bed in silence. Bernadette says "Good-night" while Amy just says "Uh-huh." After the lights are out, Amy mentions that it was flattering to have those guys send drinks over to their table. Bernadette agrees. The next morning Amy suggests that they put on hot pants and try to score some free omelets. Bernadette asks hypothetically which guy did Amy like. Amy snaps the light back on for some girl talk. Amy likes the short one with the goofy haircut. Bernie likes the tall inexperienced-looking virgin. Amy found her guy staring at her rack. For the record, underneath her cardigan is another cardigan. Bernadette says her guy sounds like Howard. Bernadette's brainy virgin sounds like Sheldon. They give each other a weird look and then say good night again.
Back at Caltech, Raj is still talking to Janine Davies who has to leave since she has kids at home. Raj says that he knows what it's like to be a single parent since he has a dog. Sarcastically she says that that is just like having kids. Raj admits that he was there to pick up a woman and instead got to sit down and talk to her on a human level. He also called her a lovely person. She wonders if he was now hitting on her which Raj denies. She calls him sweet and then again says good night. Howard comes over and remarks that she must have accepted his apology. Raj replies that they had connected and that they may have had a moment together. Howard concludes that it wasn't a moment and that even if it was, what would he do about it? After a littler bravado, he agrees that nothing will come of it.
Penny is seen in the shower glad that the police had caught that sex crazed genetically altered ape. A shadow appears on the shower curtain of a man or ape carrying an ax. Leonard is watching her movie on his computer surrounded by his shipmates. He tells everyone that they are watching his girlfriend. The gang starts chanting "Leonard! Leonard!" The curtain is pulled opened and Penny screams!
- Guest starring:
- Teleplay: Chuck Lorre Steven Molaro & Tara Hernandez
- Story: Eric Kaplan and Jim Reynolds & Steve Holland
- Oliver Sava of The AV Club gave the double-premiere a B+.
- Dhruv Rao from The DR Club gave both the episodes a B. 
- Jesse Schedeen of IGN: "…the focus was on breaking the rest of the group into pairs and sending them on different misadventures together. I enjoyed that these pairings were slightly less traditional. We rarely see Amy and Bernadette interact without Penny completing the trio… And yes, we've seen episodes focused on Sheldon pestering Penny before, but the dynamic shifted slightly as Sheldon became the one desperate for companionship…All three stories held their own, though I enjoyed the Bernie/Amy portion the most. It was nice to see these two off on their own for a change and outside the shadows of their significant other… The fact that Sheldon reciprocated Penny's hug at all is a sign of how close the two have become over the course of six seasons… this wasn't a bad start by any means." 
- The TV Critic.org: "I'll admit this made me chuckle and I was pleased to have these characters back in my life. In part that's because they all seem to have grown and matured. Sheldon is almost ready to admit that he misses Leonard and does reveal a personal secret to Penny. While she has no problem admitting the place Leonard has taken in her heart. Meanwhile Raj can now talk to other people without alcohol and actually manages to have a regular conversation with Mrs Davis."
- IMDB user reviews
- Title Reference: The title refers to the loss of Leonard in Penny and Sheldon's lives.
- Taping date: August 20, 2013.
- Chuck Lorre's vanity card.
- This episode was watched by 18.3 million people with a rating of 5.6 (adults 18-49) Including DVR users, the total number of viewers is 24.16 million, and a rating of 7.8 (adults 18-49). 
- This episode aired in Canada on September 26, 2013 with 4.311 million viewers with a weekly ranking of #2.
- In the United Kingdom, this episode aired on October 31, 2013 with 2.72 million viewers and a weekly ranking of #1.
- Episode transcript 
- Sheldon wears his Greatest American Hero logo t-shirt and a t-shirt featuring Kryptonian DNA (Sheldon has this shirt in both royal blue and drab olive green, but both appear to be unavailable).
- Amy and Bernadette attract the attention of two other guys without the gorgeous Penny around.
- Each girlfriend finds themselves liking the guy which is closer in appearance to the other friend's fellow and it scares them.
- When Sheldon says that watching Clash of the Titans was causing Penny nightmares, he had probably watched it himself since the Kraken that attacked Leonard in his nightmare is seen in that movie. Also, Sheldon previously mentioned Kraken in episode "The Date Night Variable" (S6E1) by citing the line "release the Kraken!" from Clash of the Titans.
- Both Amy and Bernadette have thier glasses off in the bedroom scene of their convention trip when they are next to each other in bed bonding to themselves (as most people don't wear glasses in bed anyway).
- Amy calls Sheldon her "Sweet Baboo", which was also Sally Brown's pet name for Linus Van Pelt in the Peanuts comic strip.
- The sailor hat that Leonard promised to give Sheldon is fulfilled in the next episode "The Deception Verification" (S7E02).
- Leonard must have learned Morse code because in "The Cooper-Nowitzki Theorem" (S2E6), Leonard claims not to know Morse code.
- In her movie clip, Penny does not look like she did in the pilot since that movie was filmed over 10 years before when she first came to California. (More like, The Big Bang Theory filmed Kaley Cuoco for the film clip for this episode (S07E01), therefore there wouldn't have been any practical way to make Penny look the way she did seven years ago as she would have looked in the Pilot episode).
- Like showing his colleagues Penny's old topless movie, in "The Bakersfield Expedition" (S6E13) he took his picture with Penny to prove to people how beautiful his girlfriend was.
- Leonard is shown with facial hair again; the first time was in "The Electric Can Opener Fluctuation" (E3E1), which also involved a scientific expedition to a remote corner of the world: The Arctic.
- The second episode where Sheldon has a nightmare of a character being attacked by a monster. The first was "The Nerdvana Annihilation" (S1E14).
- First episode where Leonard appears with none of the regular cast (The 'Howardette' couple, Raj, Penny and the 'Shamy' duo).
- This season premiere episode takes place three/four months after the last episode of the previous season.
- On Amazon prime teleplay and story credits are reversed. i.e Chuck Lorre, Steven Molaro and Tara Hernandez are credited for the "story" on Amazon's version for unknown reasons.
- The scene of the ape with the axe in the scene of Penny showering and making her scream is a reference to scene of the Alfred Hitchcock horror-movie of 1960 called "Psycho".
- Bernadette and Amy share no scenes with Penny and the four guys (Sheldon, Raj, Leonard and Howard) in this episode whereas Bernadette is on her phone to Howard once in this episode and Amy is on her phone to Sheldon once in this episode.
- Sheldon: Welcome to the exciting world of 3-D chess.
- Penny: Why don’t you admit you only want to play this game because you always play with Leonard and you miss him?
- Sheldon: You overestimate his significance in my life.
- Penny: Mmm.
- Sheldon: Do I miss how he makes a face on my toaster waffle with syrup? No. Do I miss the way he fixes the zipper on my jacket when it gets stuck? I don’t think so. Do I miss how we say good night to each other through the walls of our bedroom using Morse code? [Knocks his answer in Morse Code].
- Penny: OK, I get it. I get it. You’re an emotionless robot.
- Sheldon: Well, I try.
- Raj: Do you know I recently read a fascinating article on infidelity among penguins.
- Mrs. Janine Davis: OK.
- Raj: So if the fact that your husband left your husband makes you feel unattractive, just remember penguins get cheated on and they’re still adorable.
- Howard: It was better when you couldn't talk to women.
- Bernadette: I was thinking of going to the lecture on posterior cingulate cortex lesions in the formation of autobiographical memory.
- Amy: Oh, brain lesions are fascinating. Unless they’re yours, then they’re a drag.
- Bernadette: [Toasting] To the advancement of science.
- Amy: And to the sick and dying who make it possible.
- Penny: This is ridiculous, why am I upset just because he's off having a good time?
- Sheldon: Well, perhaps you're obsessively picturing him engaged in drunken coitus with another woman. [Penny stares at him angrily.] Is that it? Did I get it right?
- (The hotel bedroom scene of Bernadette (who is already in bed) rubbing some hand cream on herself and Amy taking her slippers off and putting them on the floor. They both take their glasses off and put them on the bedside together. Amy now gets into bed).
- Bernadette: (turning off the light) Good night.
- Amy: Mm-hmm. It was rather flattering to have strangers send us drinks.
- Bernadette: Yeah, that felt nice.
- Amy: Maybe tomorrow morning we put on some hot pants and see if we can score us some free omelettes.
- Bernadette: So, hypothetically, if, if we were to have gone with them, which one would you have picked?
- (Amy puts the light back on and she and Bernadette look at each other)
- Amy: I think I would have gone with the short one with the goofy haircut.
- Bernadette: Oh, good, ’cause I liked the tall thin one. He seemed intelligent, kind of a loner, maybe a little sexually inexperienced, like I’d have to teach him a thing or two.
- Amy: Not my guy. I caught him staring at my rack. It’d be nice to be with a man who wants to know what’s underneath my cardigan. FYI, it’s another cardigan.
- Bernadette: Your short sexed-up guy kind of sounds like Howard.
- Amy: Your brainy virgin kind of sounds like Sheldon.
- Both: (crossly together) Good night.
- (Bernadette crossly turns the light back off and both she and Amy lay back down on their pillows in a huff together).
- Penny: No. Come on, let’s talk about our lives. Tell me something about you I don’t know.
- Sheldon: I own nine pairs of pants.
- Penny: Okay, that, that’s a good start, but I was thinking maybe something a little more personal.
- Sheldon: I see. I own nine pairs of underpants.
- Penny: How about I go first?
- Sheldon: But I don’t want to know how many underpants you own. Although, based on the floor of your bedroom, I’d say it’s a thousand.
- Penny: Okay, look, here’s something people do not know about me. When I first moved out to L.A., I did a topless scene in a low-budget horror movie about a killer gorilla. Ugh! After I did it, I felt so ashamed. Thankfully, that thing never came out.
- Sheldon: I've seen that. Yeah. Serial Ape-ist. Howard found it online the day we met you.
- Penny: Oh, God.
- Sheldon: And it was literally the moment you walked out the door. But I see the type of personal revelations you’re going for. Okay, here’s one I thought I’d take to the grave.
- Penny: Okay.
- Sheldon: Hmm. A while back, YouTube changed its user interface from a star-based rating system to a thumbs-up rating system. I tell people I’m okay with it, but I’m really not.
- Penny: That’s your big revelation?
- Sheldon: Yes. Whew, I feel ten pounds lighter.
- Leonard (on board boat, at a party, dancing): Excuse me, ladies, my pants are buzzing. North Sea, how can I "kelp" you?
- Penny: Leonard?
- Leonard: Penny? Hey, it’s Penny. Everybody say hi to Penny.
- Everybody: Hi, Penny!
- Penny: Wow, it sounds like you’re having a good time.
- Leonard: Best time of my life.
- Sheldon: Isn't it five thirty in the morning there?
- Leonard: Is it? Hey, everybody, it’s five thirty in the morning!
- Penny: Uh, okay, well, we were just calling you because we were missing you.
- Random voice: Iceberg!
- Leonard: Uh-oh, hang on.
- Sheldon: Are you in danger?
- Leonard: No, it’s a drinking game. Whenever we see an iceberg, we take a shot!
- Everybody: Berg! Berg! Berg! Berg! Berg! Berg!
- (The scene of Bernadette and Amy's conversation after their toast at the bar)
- Bernadette: This is fun. We never really get to talk shop with Penny around. We usually just end up talking about boys.
- Amy: Which is fine, but it’s nice to mix it up with a little intellectual conversation.
- Waiter: From the two gentlemen at the bar.
- Amy: Oh, my gosh, boys bought us drinks, boys bought us drinks. Thank you, thank you, thank you so much.
- Bernadette: Be cool.
- Amy: You be cool. Guys are hitting on us, and not just to get to Penny.
- Bernadette: You’re right. Thank you.
- Leonard: Sheldon, it’s not a great time, what do you want?
- Sheldon (in the apartment): Hello to you, too. I’m sorry, but this is important.
- Leonard: What is it?
- Sheldon: Back to the Future II was in the Back to the Future III case, and Back to the Future III was, get this, in the Back to the Future II case.
- Sheldon: So, did you do that, or am I in the house with an intruder?
- Leonard: Sheldon, I got to go inside. It’s getting rough out here.
- Sheldon: You’re dodging the question, I knew it was you. (Kraken roaring)
- Sheldon: What was that?
- Leonard: What was what?
- Sheldon: This isn't a very good connection, but it sounded like someone just released a kraken.
- Leonard: Okay. I'm hanging up now. You know there's no such thing as a... (Got dragged overboard by a kraken tentacle)
- Sheldon: (wakes up) No!
- Penny: (in film taking a shower) Ah, I'm so glad the police finally caught that psychotic, genetically engineered ape.
- Leonard: That is my girlfriend, I swear to god.
- Shipmates: (chanting) Leonard, Leonard, Leonard, Leonard.
- (Penny sees the man in the ape suit opening shower curtain (he is holding an axe in a parody of 'Psycho') and screaming in film)
- (Scene: A hotel room)
- Bernadette (on phone): Howie, stop. I can’t talk like that. Amy’s right here.
- Amy (on phone): Sheldon, stop. For the last time, I will not bring home bed bugs.
- Bernadette: The hotel’s nice. There’s a pool, a gym, the bar looks like fun.
- Amy: Because I looked in the bed, and there are no bugs.
- Bernadette: Aw, I love you, too. If I don’t talk to you before you go to sleep, I’ll meet you in dreamland.
- Amy: Good night. No, I will not consider sleeping in my garment bag.
- (Amy now puts her phone down on the desk in disgust)
- Amy: So what happened? How’d it go?
- Bernadette: It’s fine. I thanked them again and let them know we’re not available.
- Amy: So I can drink this without having to give up the goodies?
- Bernadette: Yes, it’s all cool. Although, if you wanted to talk to one of them, no one would blame you.
- Amy: And why would no one blame me?
- Bernadette: I don’t know what I’m saying.
- Amy: Well, it sounds like you’re saying that I could do better than Sheldon.
- Bernadette: (not happy by the taste of the drink) Boy, these drinks are strong. Hoo, mama, I’m gonna be huggin’ the toilet tonight.
- Amy: No, tell me, I want to know what you meant by that.
- Bernadette: I just meant that you’re not married and your boyfriend’s kind of, Sheldon.
- Amy: And your husband is extremely Howard. What’s your point?
- Bernadette: Sorry. I have no point. That was a stupid thing to say. (she changes the subject) Can we please just go back to having a nice time?
- Amy: We could, but unfortunately my brain is lesion-free and I remember that rotten thing you just said about my sweet baboo.
- Bernadette: (calmly and crossly) Come on. I apologize. Can we please just let it go?
- Amy: Sure.
- Bernadette: Thanks.
- Amy: Your husband’s weird and his clothes are ridiculous.
- (Bernadette starts to stare crossly at Amy)
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