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Sheldon and Amy are streaming a live "Fun with Flags" on-location from Penny's old apartment. Raj and Howard or "Footprints on the Moon", are the new house band providing music and they sing the new "Fun with Flags" theme. Since the two hosts are co-habitating, the theme of the show is areas that come together like St. Kitts and Nevis. Penny, Leonard and Bernadette are watching the show in apartment 4A where Bernie drops the bomb that Amy's apartment has been fixed for weeks. Leonard was shocked that Amy was lying to Sheldon though he lied to Sheldon to get him out.
Raj and Howard leave with Sheldon's gratitude though Raj is annoyed that they didn't get paid or even a sandwich. Amy asked what Sheldon wants for dinner and he suggests that they get Thai food and swing by her apartment to check it out. Amy is nervous and counters that he would not like that since it's a construction zone with stray nails and butt cracks. Sheldon wonders if she keeps changing the subject on purpose which she denies and then gets him to start a lecture on kings and their subjects.
At the Caltech cafeteria, the guys are discussing JPL's plan to catch an asteroid that might hit the earth. Sheldon is uncharacteristically quiet because he thinks that Amy is acting a little odd. Howard wonders what Sheldon considers to be odd. It was her behavior that was bothering Sheldon and he feels that she is keeping something from him. It bugs him since he shared his body with her AND his Netflix's password. Leonard tries to reassure him that it is nothing bad. Her apartment had been ready for a couple of weeks and she was enjoying living with him so much. Sheldon then felt both hurt and flattered. Howard then tells Leonard that he knows that Penny is doing something behind his back. Penny has been secretly moving his collectibles to storage for weeks.
Sheldon and Leonard are discussing their significant others lying activities including the Spider-man figure that had disappeared from Leonard's desk. The girls show up with the food and Sheldon immediately asks Amy about her apartment. Amy says that it still being worked on and Penny says that is still a mess. They swung by and saw it. Sheldon is now confused. He asks Leonard in Klingon if he thinks Penny is lying. He doesn't know. Amy then asks Penny in her secret language Ubu Dubbi whether she thinks that Leonard knows. Maybe. Sheldon then curses in Klingon and Penny demands to know what is going on. Leonard explains that Sheldon knows, but wants to know why Penny says that she saw the apartment. Amy admits that Penny is covering for her since they finished two weeks ago. Sheldon wants to know how Amy can lie to him. Penny butts in that she had enjoyed living with him because she was in love. Leonard wants to know what it is called when you secretly get rid of your husband's stuff. That is NOT true! Leonard explains that Bernadette told Howard, Howard told him and he can see the results. Penny then gets upset that he'll believe his friend, his friend's wife and his eyes over HIS wife. Wow! Penny is sure that her husband wouldn't notice especially since he is missing his Batman on his key ring. Howard, Bernadette and Raj arrive and they get yelled for their part in this conspiracy. Amy then apologizes to Sheldon, while Raj asks them if they plan to keep living together. Sheldon considers is a positive experience. Amy asks if he still wants to. Sheldon agrees. Amy gasps when Penny tells her in Ubu Dubbi to be cool. She changes her response to "Whatever." Howard suggests that Leonard keep his stuff in Sheldon's old room which bothers Sheldon. That's my room. Everyone keeps telling him that he ISN'T going to be living there anymore.
Sheldon and Amy are getting into bed and she appreciates him understanding. Sheldon thinks that everyone wants to spend more time with him. He also wonders where they might live. Apartment 4B, Amy's Apartment, somewhere else. Amy finds it kind of exciting since they could move wherever they want. Sheldon then starts to worry about smokers, pets, mold, traffic noise, bus routes... Amy starts to hum the "Star Trek" theme. Sheldon does not consider himself a child. Try the "2001: A Space Odyssey" theme. He finds that soothing as he turns over and Amy cuddles up to him. Amy really knows her boyfriend.
As they get ready for bed in Apartment 4A Leonard tells Penny that she can make the bedroom really feel like hers and he presents to Penny her own pink Power Ranger action figure. Penny is happier about the room plans over her new toy. Leonard wants to know what of his he is going to keep. She replies a candle and HIM.
Sheldon is tossing and turning. Amy asks him what is wrong? He is having a struggle about leaving his old bedroom so he wants to check it out. Entering the living area he hears some music. Entering his room, he finds a stone wall with Leonard strapped to the wall and Penny dresses in leather holding a whip.They turned his room into a sex dungeon as Penny whips Leonard. Sheldon screams and wakes up next to Amy. It was a dream.
Back at the comic book store, Howard wants to know how Leonard was dressed in Sheldon's dream. Sheldon wants help with the decision he has to make about moving. Leonard does not want him moving back in. They ask him if he loves Amy. Yes. They ask him if he enjoyed living with him. Yes. Sheldon complains that they are not helping him.
Sheldon approaches his 4B and then stares are 4A standing right in the middle of the hall. Amy shows up and asks him what was going on. He is contemplating Buriden's donkey. A hungry donkey left between two equidistant bales of hay will starve to death while trying to make a decision. Amy understands his dilemma and starts to discuss it compared to other's experiments. Sheldon gets into her discussion and then follows her into their place.
Penny shows Leonard his new bedroom. He exclaims: Wow. He wants her to have the bedroom she wants. They exchange "I love you"s though Leonard looks distrait. Leonard then hides some of the new stuff in Sheldon's bedroom and tells him to not tell Penny.
- Guest starring:
- Teleplay: Steve Holland, Jim Reynolds & Adam Faberman
- Story: Steven Molaro, Eric Kaplan & Maria Ferrari 
- Title Reference: Amy stretching the truth about her old apartment being repaired.
- Taping date: October 18, 2016
- This episode was watched by 14.18 million people with a rating of 3.1 (adults 18-49).
- Total viewers including DVR users 19.63 million.
- The Big Bang Theory was ranked #7 for the week ending 6 November 2016.
- This episode aired in Canada on November 3, 2016.
- Chuck Lorre's vanity card 
Caroline Preece of Den of Geek - It's also a funny episode, bringing the whole cast together to bounce off each other in that special way they do when everything's working. From Howard and Raj's new role as the 'Fun With Flags' house band, to the secret languages battle near the end and the revelation that Penny has been slowly putting Leonard's collectibles in storage, it all zips along with an energy that's been missing in an otherwise strong season.
- First Fun with Flags episode from Apartment 4B. Also, first time the show has an opening theme, played by Footprints on the Moon.
- Footprints on the Moon, Howard and Raj's group, play on "Fun with Flags".
- The plumbing in Amy's Apartment has been repaired.
- Penny puts Leonard's collectibles into storage, prompting him to realize that she doesn't really feel at home just yet.
- Humming Sheldon to sleep, Amy has learned how to control Sheldon better than Leonard ever could. Although, Amy didn't sang Soft Kitty, the lullaby that almost always make him sleep.
- Penny begins to redecorate the apartment, starting with the bedroom she shares with Leonard.
- Big Bang nerd definition: veracity - habitual truthfulness.
- First time, Amy and Penny shares an Ubbi Dubbi - Amy's secret language- conversation on screen. Although in "The Skank Reflex Analysis", Amy talked to the blonde girl about teaching her her original secret language: "Op".
- Sheldon agrees to live with Amy permanently though the location is yet to be decided.
- The Ubbi Dubbi language came from the 1990s PBS Kids show, ZOOM.
- Sheldon: I'm concerned about Amy. She's acting a bit odd lately.
- Howard: Just out of curiosity, what registers as "odd" to you?
- Sheldon: Why would she keep something from me? I shared my body with that woman... and my Netflix password!
- Howard: You know, if he moves across the hall for good, Leonard can keep all the stuff you don't like in Sheldon's old room. That solves everything.
- Penny: That's a great idea!
- Leonard: (intrigued) Ooh! Maybe I could turn it into a gaming den!
- Raj: (impressed) That would be amazing.
- Sheldon: (concerned) Wha-no-what-wha-no, excuse me? That's my room.
- Leonard: But, you won't be living here.
- Sheldon: But, that's my room.
- Leonard: You won't be living here.
- Sheldon: But, that's my room.
- Leonard: (to the gang) You guys might wanna start eating. (to Sheldon) You won't be living here.
- Penny: Sweetie, once you stop paying rent, none of this is really yours.
- Sheldon: (sadly) But, that's my room.
- Everyone Else except Bernadette: (annoyed) BUT, YOU WON'T BE LIVING HERE!
- Sheldon: Hello, I’m Dr. Sheldon Cooper.
- Amy: And I’m Dr. Amy Farah Fowler.
- Sheldon: And welcome to the first “on location” episode of Dr. Sheldon Cooper and Dr. Amy Farah Fowler present:
- Both: Dr. Sheldon Cooper’s Fun with Flags.
- Sheldon: Hit it.
- (Raj and Howard start singing)
- Howard: ♪ ♪ For joy and fun, there’s no better manner than to fly a pennant, flag or banner. ♪ ♪
- Raj: ♪ ♪ What fills my heart and makes my eyes moist. Sending a flag up a pole on a hoist. ♪ ♪
- Both: ♪ ♪ Fun with Flags. Fun with Flags. ♪ ♪
- Howard: ♪ ♪ Oh! Say can you see. ♪ ♪
- Raj: ♪ ♪ It’s Fun with Flags. ♪ ♪
- Both: ♪ ♪ Fun with Flags. ♪ ♪
- (theme song ends)
- Amy: As you may notice, just one of the changes around here is our new house band.
- Howard: [Piano melody.]
- Sheldon: Who haven’t learned their place yet.
- Amy: We’re also coming to you live from a different apartment.
- Sheldon: Dr. Fowler and I began and experiment in living together after her apartment became water damaged. This is our friend Penny’s place. You may remember her from our episode “Flags: And the People Who Don’t Understand Them.”
- Amy: So in the spirit of cohabitation, the theme of today’s episode is flags of two regions coming together as one. Such as the flags of St. Kitts and Nevis.
- Sheldon: So , let’s roll up our “sleevis “ and get to know Nevis.
- Howard: [Piano ba-dum.]
- Sheldon: Well, I like that, but next time check with me.
- Amy: Did you know that the flag was designed by a student Edrice Lewis…
- Sheldon: Buda and Pest united to form Budapest. And that’s why Budapest is “Budabest”. Now.
- Howard: Oh, right. [Piano ba-dum.]
- Sheldon: You know, if you like, I could call your landlord and complain.
- Amy: Thanks, but you don't have to.
- Sheldon: Oh, I don’t mind, I’m very good at complaining. If it were an Olympic sport, I’d complain about what a stupid sport it is and then I’d take home the gold.
- Amy: Good stuff.
- Amy: I’m sorry I lied about my apartment.
- Sheldon: It’s all right.
- Leonard: And?
- Sheldon: And what?
- Penny: Your wizard robes are next to go.
- Raj: Now that everything’s on the table, you think you two will keep living together?
- Sheldon: Despite recent events, I consider our experiment in cohabitation to have been positive.
- Amy: Are you saying you’d like to live with me?
- Sheldon: I’m open to the possibility.
- Amy: [Gasps.]
- Penny: [Speaking Ubu Dubbi] Amy be cool.
- Amy: Whatever.
- Sheldon: If we did continue to live together, would it be here?
- Amy: I don’t know. It could be.
- Sheldon: Of course there’s, there’s always your apartment.
- Amy: Sure, sure, we could live in my apartment.
- Sheldon: I hate your apartment.
- Amy: Sorry, you brought it up?
- Sheldon: Well, I suppose we could find a whole new place. You know, and, technically, we don’t have to stay in Pasadena. We could, we could move to Altadena..or a place that doesn’t end in “dena”.
- Amy: It’s kind of exciting. I mean… we could do whatever we want.
- Sheldon: What on earth. [Enters his old room, which now is used for sex.] What is going on?
- Leonard: Oh, hey Sheldon.
- Penny: We turned your room into a sex dungeon. [Whips Leonard.]
- Leonard: Oh!
- Sheldon: No! [Wakes up screaming.]
- Amy: What happened?
- Sheldon: Gentlemen, please this is a significant decision. Now, do Amy and I continue living together? Or do I move back in with Leonard?
- Leonard: Over my assless chaps you will.
- Howard: This isn’t complicated. Do you love Amy?
- Sheldon: Yes.
- Raj: Do you like living with her?
- Sheldon: Yes.
- Leonard: Do you know what you need to do now?
- Sheldon: Apparently I must figure this out on my own ‘cause you guys are no help at all.
- Sheldon: Are you going to confront Penny?
- Leonard: Eventually, I guess. Although I am kind of curious how long she thinks she can keep hiding my stuff without me knowing.
- Sheldon: Hmm. You know. Perhaps instead of confronting them, we should see how far they’re willing to spin their tangle webs. Like that Spider-Man action-figure that used to be on your desk.
- Leonard: Oh, my God I’m going blind.
- Penny: Hi. Food’s here.
- Sheldon: Oh. Excellent. I’m very hungry. Yeah, speaking of which, what’s going on with your apartment?
- Amy: Oh, uh, they’re still working on it.
- Sheldon: Interesting. Very interesting.
- Penny: Yeah, we swung by her apartment on the way to the restaurant, and they’re gonna be fixing it for a while.
- Sheldon: Wait, uh…you saw her apartment?
- Penny: I did. Still a mess.
- Sheldon: Leonard.
- Leonard: Yeah.
- Sheldon: [In Klingon] I don’t understand. Is Penny lying?
- Leonard: [In Klingon] I’m not sure.
- Amy: Why are you speaking Klingon?
- Sheldon: Why are you speaking English?
- Amy: This is ridiculous. Penny, do you remember when I taught you Ubbi Dubbi?
- Penny: [In Ubbi Dubbi] Absolutely I do.
- Amy: [In Ubbi Dubbi] Excellent. Does Sheldon know I’m lying?
- Penny: [In Ubbi Dubbi] If Leonard told him it’s possible.
- Sheldon: Oh, wait, stop that.
- Amy: You stop that.
- Sheldon: [In Klingon] Do you understand them?
- Leonard: [In Klingon] No.
- Sheldon: [In Klingon] Damn it!
- Penny: Okay. That’s enough. You know what? What is going on?
- Leonard: Fine, I told Sheldon that her apartment’s been finished, but then you just said it’s not, so now I’m all confused.
- Amy: Penny was just covering for me. My place has been ready for two weeks.
- Sheldon: How could you lie to me?
- Penny: Uh, she’s enjoyed living with you. It’s called being in love.
- Leonard: Hmm. And what’s it called when you secretly get rid of all your husband’s stuff?
- Penny: What...That is not true!
- Leonard: Wh-wh-wh…Bernadette told Howard, Howard told me. Plus, I can see all my stuff is gone.
- Penny: Oh, so, you believe your friend and your friend’s wife and your own eyes over me? Wow.