Sheldon and Amy are presenting a live broadcast of Fun with Flags, with Howard and Raj again providing the music. This episode is a retrospective which starts with interviews with Leonard and Penny. Leonard can’t remember when it started, while Penny tells him to find someone interested in flag trivia. Opening up the phone lines, no one calls for a while until they hear from Bert, the geologist. He has a new girlfriend. Sheldon hangs up on him, but he calls back to let them know that his name is Rebecca.
Howard, Bernadette, Halley and Stuart are heading for an outing at the zoo. Bernadette is checking on the website for Halley’s day care center and is worried about leaving her with strangers even though it is very near Howard at Caltech.At the cafeteria, Sheldon wants to tell physicist jokes since Howard wasn’t there though Leonard and Raj aren’t interested. Bert stops by and Leonard brings up his new girlfriend. They get invited over for dinner with the gang, which is fine with Sheldon after he learns that she isn’t a geologist.
At sloth exhibit at the zoo, Bernadette learns that they take care of their young for a whole year, while she’s returning to work after only four months.
Stuart is making dinner in the kitchen as Bernadette arrives finally getting Halley down to sleep. Howard suggest that if she’s not ready to go back to work, they could work something out. Bernadette says that she’ll be fine. Stuart adds that it’ll be good for Halley since they wouldn’t want her to turn out like Mama’s Boy Howard.
Back in 4A, they are talking to Rebecca as Sheldon returns from a time-out. Sheldon apologizes. Rebecca and Bert met on a geology dating site. He did much better after he added that ne won a substantial cash grant from the MacArthur foundation. Rebecca almost immediately contacted him. With Rebecca gone, Amy asks Bert if he’s worried she’s only with him for his money. Bert hopes so since he bought her a huge flat-screen TV on their first date.The whole Wolowitz household starts crying as they get Halley ready for her first day at daycare.
Back in the university cafeteria, where Sheldon tells them another physics joke, Bert joins them. Raj apologizes for last night. Bert realized that he shouldn’t use his money to find love. He might break up with Rebecca and hold out for a hot blonde who lives him for himself.
At the day care center, Howard first shows Bernadette that Halley is setting in fine. He watches Halley until he jumps as Stuart sneaks up on him. Knowing that it would be weird to stand there all day, Stuart and Howard decide to take her to the aquarium instead.
As the gang has dinner, Sheldon is reading comments on their Fun with Flags retrospective. Bert joins them, says he misses Rebecca and doesn’t know why he listened to them. Penny tells him that he is a good guy and deserves someone interested in him instead of his money. Leonard says that he can always call her, but she is not returning his messages.
Back at home, Stuart and Howard arrive with Halley and insist they’ve just come from daycare, but they called Bernadette when they took Halley out.
- Guest starring:
- Teleplay: Steve Holland, Tara Hernandez & Jeremy Howe
- Story: Steven Molaro, Jim Reynolds & Maria Ferrari
- Title Reference: Refers to the difficulty that Howard, Bernadette and Stuart had in being "separated" from Halley while she was at daycare.
- Taping date: March 28, 2017
- This episode was watched by 11.89 million people with a rating of 2.5 (adults 18-49).
- Total viewers including DVR users 16.49 million.
- The Big Bang Theory was ranked #x for the week ending xx April 2017.
- This episode aired in Canada on April 13, 2017.
- Chuck Lorre's vanity card .
- Caroline Preece at Den of Geek! - The set-up of The Separation Agitation is that Bert has an unlikely new girlfriend, and she’s clearly using him for his money from the recent research grant (impressive continuity for this show)...The characterization of Rebecca was basically what could have easily happened had the writers not liked Penny so much. The two women’s similarities were more or less lamp shaded within the episode, and it just made me glad that this wasn’t the road they went down with ‘ditzy neighbor lives across the hall from nerds’.... also quite like the slight role reversal of Howard being the one to take her out of daycare to spend the day playing hooky - as much as the show is showing Bernadette to have anxiety about being a working mother... 
- Howard imitates both Stuart and Bernadette.
- Howard and Stuart have a hard time letting Halley go just as Bernadette did in the previous episode.
- Footprints on the Moon appears.
- Bert still has his grant money.
- Bert's new girlfriend is allegedly a gold digger like one of Raj's previous girlfriends. Played by April Bowlby who was a regular on Two and a Half Men also produce by Chuck Lorre. She played Kandi who dated Charlie and married Alan.
- Sheldon says Leonard and Penny have nothing in common, but this is false. They actually do have a few things in common:
- They each have one brother and one sister
- They had issues with the opposite gender parent growing up
- Another possibility is them being the second born child and their sisters being the first born and their brothers the third born
- Another possibility is both of them always willing to try new things
- Another possibility is them wanting to be social and wanting to make friends with people
- Raj: Sheldon, what did Amy have that attracted you?
- Sheldon: Oh, so many things: her mind, her kindness, and especially her body.
- Raj: Really!
- Amy: Relax. We're the same blood type; he know he could harvest an organ.
- Sheldon: All right, we're about to go live. Everyone on their A game. [claps] Good energy... [flatly, to camera]
- Sheldon: Hello. I'm Dr, Sheldon Cooper.
- Amy: And I'm Dr. Amy Farrah-Fowler.
- Sheldon: And welcome to a special retrospective, where we will take a look back at the history of Fun with Flags on an episode we're calling Sheldon Cooper, Amy Farrah Fowler: Fun with Flags: Behind the Flags, a Retrospective.
- Raj: I feel bad for Bert.
- Sheldon: So he's using his money to attract a mate. Is that any different than me using my intelligence to attract Amy, or Leonard using his power of grovelling to get Penny?
- Leonard: Totally different. Bert's money might run out, but I can beg until the end of time.
- Penny: All that, *and* he's shorter than me.
- Sheldon: Hello. I'm Dr, Sheldon Cooper.
- Amy: And I'm Dr. Amy Farrah-Fowler.
- Sheldon: Based on the glowing reception of our recent Behind the Flags Retrospective we thought you might like to see how it all came together
- Amy: So welcome to tonight's episode: Sheldon Cooper, Amy Farrah Fowler: Fun with Flags: Behind the Behind the Flags, a Retrospective Retrospective.
- Sheldon: Oh, we already have our first call!
- Amy: Oh. Hello, you're on Fun with Flags.
- Bert: The jet-ski worked. I got her back.
- Bernadette: What if she likes these people more than us?
- Howard: She already likes bubbles more than us.
- Howard: How about after this we go to the exotic bird show?
- Stuart: Not a good idea. My hair is prime nest building material.
- Howard: What are you making?
- Stuart: Chicken. Birds mess with my hair, I come back hard.
- Sheldon: [after Bert introduces Rebecca] She's younger and far more attractive than he is. [to Leonard and Penny] They're copying you two.
- Sheldon: Bert, Rebecca, I'd like to apologize for my insensitive comment earlier.
- Rebecca: Don't worry about it. It's fine.
- Sheldon: See, it was fine. I didn't need a time out.
- Amy: It wasn't a time out. Let's get some food.
- Sheldon: You made me sit on the stairs and think about what I did...
- Amy: [Nudges Sheldon] I said get your food!
- Howard What are you doing here?
- Stuart: Can't a guy hang out at a college he doesn't go to and stare at a baby that isn't his?
- Amy: I'm sorry, Bert, but aren't you worried she's only with you for your money?
- Bert: She'd better be. On our first date, I bought her an 80-inch flat screen.
- Sheldon: Your first date? Did you even measure her walls?
- Leonard: Don't you have a friend you can set him up with?
- Penny: Hey, I already set up Howard and Bernadette. It's your turn to ruin some poor girl's life.
- Rebecca: Where's your bathroom?
- Leonard: Just down there. [Rebecca leaves]
- Bert: She's so perfect, sometimes I think she isn't real. And then she goes to the bathroom, and I know she is.
- Penny: Aww, that's so weird.
- Raj: I'd love a personal trainer. I haven't seen my abs since they opened a Shake Shack on my drive home.
- Rebecca: I can give you some free sessions.
- Penny: Oh, is that offer for everybody?
- Leonard: Nice try. I'm not going.