The episode starts with J.D. and Kim lying in bed and getting to know each other better. They spend the next three weeks getting their apartment ready and back together.
Elliot and Keith are discussing the wedding and the fact that their families can't sit together because the last time they did, Elliot's mom slept with Keith's uncle Ronald. She apologizes for being a bridezilla, then orders him to try on the tux Elliot picked out. She then confronts the Janitor about not RSVPing for the wedding, who confirms. They hug.
Dr. Cox is still upset about J.D. being the godfather for Jennifer. She tells everyone that the christening ceremony will be in the hospital chapel and calling Jennifer "J.D." before leaving. This sends Cox into a towering rage.
J.D. and Kim are visiting Turk and Carla. Kim announces her apartment lease is up in Washington, and J.D. wants their son to stay in the area for a few months.
Keith and Elliot are still discussing the wedding. She points out that comfort isn't an option when all their closest friends and family are together, and that the wedding is about her. Elliot then checks on Carla and Mr. Cole, who's in a persistent vegetative state and being taken care of by his wife.
In Coffeebucks, the Janitor has gathered the Brain Trust (Todd, Ted, and Lloyd) to help him get Elliot a good gift for the wedding. Doug asks what's going on and Janitor is giving Lloyd a trial run.
Kim tells J.D. that her hospital in Tacoma will only give six weeks maternity leave absence. He tells her to apply for the Urology job at Sacred Heart, since Kelso hates the new Urologist.
Dr. Cox offers to stop calling J.D. girls' names in exchange for him not being godfather. He holds out, and Cox offers to give him his real pager number. That not working, he will give him one hug. Per Year. J.D.'s about to seal the deal, but stops knowing that being godfather is lifelong.
Elliot praises Mrs. Cole for taking care of her husband for two years. Seeing Mrs. Cole take care of her husband, Elliot starts to think.
Janitor is still working with the Brain Trust on getting the perfect gift. Doug tries to force his way back in, but fails. Janitor wants to give her joy, happiness. Ted points out that they can't control what kind of husband Keith will be, giving Janitor an idea.
Kelso tells J.D. that Kim can have her job back. While J.D. goes off to finish his godfather speech, Cox pleads with Jordan to oust him as godfather. She gives him the terms of him and Jack having to wear matching outfits when she buys them and one date a month with the maitre'd at the Italian restaurant they go to. Cox immediately ousts J.D. as godfather.
At the christening, Jack is the godfather while Cox picks Carla to be godmother. The father makes a speech about spending their lives together and bringing a child into this world. Elliot and J.D. now both look worried.
J.D. tells Kim that he has to cover a shift, but really needs to be alone. He lies down in the on-call room, and finds Elliot in there hiding from Keith. She told Keith she was working and he left, but in reality has been kidnapped by the Brain Trust. She's freaking out because the engagement's only lasted two months and claims to be the biggest idiot in the world. J.D. counters with everything he's done for Kim.
In the lounge, the Brain Trust tells Keith that Janitor's gift to Elliot is to train Keith to be the perfect husband. Janitor and Ted offer advice, but when Lloyd comes up short, Doug's hiding behind the vending machine pointing out how bad Lloyd is at this.
Back in the on-call room, Elliot explains why she freaked out. J.D. reassures her that she'll feel that way about Keith one day. He wonders aloud if they're freaking out about nothing and if they are with the right people. He thinks back to something simple he and Kim have in common, but Elliot snaps him out of it. He tells Elliot that he confided in Kim that he worries about being a dad and a doctor, because both require all of all of yourself into them. Elliot explains that she's never felt this much love and that Keith would walk through fire for her.
In the lounge, Keith says that he wouldn't walk through fire to prove his love for Elliot. Janitor gives a role play scenario of something that could happen, but the Todd ruins it. Keith gets angry and tells the Trust that the only person he has to prove his love to is Elliot and leaves. The Brain Trust puts their hands in, and Janitor kicks Lloyd out.
In the on-call room, J.D. and Elliot are now lying in bed together in scrubs. He tells her that her in scrubs reminds him of when they dated. J.D. asks if they're perfect for each other, but have the same fatal flaw. Elliot says she's reached the point of no return, and J.D. says the same thing. Elliot tells J.D. she'd have to do something huge to get out of this. J.D. tells her he'd have to go nuclear.
The episode ends with the camera panning through all the couples: Turk and Carla on their couch drinking wine, Cox and Jordan sitting on their couch talking and laughing, Keith sitting alone, Kim sitting alone with her half-glass of wine, and then to J.D. and Elliot, still in bed. Elliot grabs J.D.'s hand, both exchange a quiet "Hey", and turn to face each other, and move closer...