Dr. Kelso tells J.D. and Dr. Casey (Michael J. Fox) that some patients are complaining about a weird noise. Upon further investigation, it turns out to be a lone toilet on the roof. The Janitor reveals to J.D. that it is his secret epiphany toilet, where you can get away, just think and usually solve your problems. He swears J.D. to secrecy, who automatically tells everyone about it. Casey is particularly intrigued by the toilet, because it represents a challenge he may not be able to overcome, sitting on a toilet that's out in the open, totally exposed. He always goes to the bathroom at home, so using another toilet would be a major accomplishment.

Kelso asks Cox to find a bed for his sick gardener, Hector. Since Kelso closed one of the wings, there isn't any empty bed to be found. But, while sitting on the epiphany toilet, Cox has an idea. Much to Kelso's dismay, he puts Hector in a bed in Kelso's office. When it becomes too crowded in Kelso's office, Cox and Carla transfer Hector to the closed wing, forcing Kelso to re-open it.

When Elliot mistakenly intubates a tube into a patient's stomach, instead of his lungs, almost killing him, her already shaky confidence gets worse. She has Dr. Cox intubate the next patient. Suddenly, Dr. Casey appears before her like a beacon in the night. Hoping that he will help her like he's helped everyone else, Elliot is later disappointed when Kevin suddenly leaves Sacred Heart to return to his own hospital.

Her disappointment turns to surprise, when she finds toilet paper attached to her shoe. Attached to the paper is a note instructing her to follow the paper trail. It leads to the roof. On the end of the paper trail is a Polaroid photo of Casey sitting on the epiphany toilet, his hands raised in victory. Her turn is next. While sitting on the toilet, she has a fantasy where a helicopter lands on the roof, the patient needs intubating, she hesitates. Then, one of the paramedics is revealed to be Dr. Casey, who tells her that sometimes you have to just dive in and do things. Her next intubation goes perfectly.

Carla and Turk ask J.D. to be their best man. He gladly accepts. But, he later hears a message that Turk's brother left, saying that his business trip was cancelled, so he can be Turk's best man after all. Turk has an epiphany while on the toilet - he knows he just has to let J.D. down easy. But that doesn't happen when J.D. goes on and on about all the work he has to do to prepare for his best man duties. But later, he confesses to Turk that he knows he wasn't first choice, and he's happy to step aside. They later agree that J.D. and Turk's brother will be co-best men.