In the Scrubs series finale tears are shed, laughs are shared, confessions are made, disputes are resolved, and hugs that should have been distributed years ago are finally given.
Morning Sex
J.D.’s finale begins in the same place his career with Sacred Heart began eight years ago.  He wakes this morning next to Elliot and thinks back to his first day and all the things that happened then.  He remembers hiding with Elliot in the supplies closet, Kelso’s first unkind words to him, and the time Janitor accused him of sticking a penny in the door, sealing it shut.  J.D. tries to use the fact that it’s his last d ay to score some morning sex, but Elliot isn’t having it.  She tells him that she moved her bed into his apartment, and J.D. realizes that she’s been “sneak-moving” into his new place.  Eventually, J.D. gets his morning sex.
Bitter Roast
Ted’s coffee cup is full of dirt because Kelso told the coffee guy that Ted was talking shit about the coffee.  Kelso has taken steps to go back to doing part time clinical work.  The new gig will keep him traveling and doing what he misses doing.  He asks for one final muffin, and asks someone to distract the coffee shop manager while he steals his favorite table from the joint.
Spinning Eagle
J.D. pulls up to Sacred Heart with Elliot to begin his last day.  Elliot says she isn’t going to say goodbye to him because she knows if she does she’ll begin to cry, which she begins to do anyway.  Turk has placed a giant canvas sign across the entrance to the hospital which reads: GOODBYE J.D.  The sign is blocking the stairs, so people have to go around.  Turk has also set up a gymnastics-matt so he can give J.D. a final “Spinning Eagle”.
Later, Turk gives J.D. a goodbye hug and J.D. comments that he smells like a weight-lifter.  Elliot and Carla try to see what it’s like to hug each other the way their men hug each other and find it interesting.
The Tao of Cox
J.D. wants his moment with Dr. Cox and can’t wait until the end of the day to get it.  He approaches Cox and thanks him for making him the man he is today.
“You can’t blame me for that!” Cox defends.
“That’s too mean,” Jordan agrees.
J.D. hands Cox a thick, leather-bound, manuscript.  J.D. explains that he wrote down every rant/ speech Cox has made in the past eight years and copied them into this book.  Each rant is accompanied by a number between one and five, which is a way of ranking how much the rant had hurt J.D.’s feelings.  Fives hurt him the most.  Cox, in his typical, insensitive way, tells J.D. that he doesn’t care about the book, and leaves J.D. without his hug.
Mrs. Stonewater argues with J.D. but it turns out she is delirious.  Her son, Dan, is confused as to what’s wrong with her.  J.D. assures him they’ll get to the bottom of things.
Not a River in Egypt
Janitor approaches J.D. with a thought provoking query: “can there be good without evil?”  He then confesses that he spent the previous evening bowling with M. Night Shamalan.  Needless to say, J.D. harbors a few doubts.  Janitor has prepared something special for J.D.  He pulls a necklace out from under his shirt, where there is a penny hanging from the end of the chain.  Janitor claims that it is the same pen ny J.D. had used to jam the door on his first day at Sacred Heart.  For the hundredth time, J.D. denies that he had anything to do with it.  Janitor demands that he confess, but J.D. won’t.
A nurse hands J.D. a chart and after taking a somber look at it, J.D. realizes it’s time to ruin someone’s day.  He explains to Dan that his mother has Huntington’s disease, a genetic disorder caused by a faulty gene which causes changes to mental stability and personality.  The disease has no cure and, once onset, is fatal.  J.D. mentions that since Dan’s mother has it, there is a 50-50 chance that he has it also.  An exam could determine whether or not Dan will get the disease, but it cannot determine when in life it will strike.  When asked if he wants to run some tests, Dan asks to hold off on finding out if he will be afflicted by the disease.
Later, after Janitor tries to get J.D. to confess to the penny fiasco again, Dan tells J.D. that he doesn’t want to take the test for now.  J.D. can’t understand why anyone wouldn’t want to know about something if it could potentially kill them, and resolves to later ask Dan why he declined taking the test.  Cox advises J.D. to say nothing.
False Alarm
Besides Elliot and Turk, no one has made an attempt to say goodbye to J.D. Dorian vents his frustration to Elliot in the parking lot.  Elliot motions to the window where the staff of Sacred Heart has gathered to wave goodbye… to Kelso who throws a coffee-shop table in the trunk of his car.  It turns out that Turk sign has also been altered to read: GOODBYE BOB.  J.D.’s feelings are hurt, and Bob Kelso asked him what he thought leaving this place would be like.  A brief fantasy shows that J.D. had imagined that the whole place would fall apart when he left Sacred Heart and flipped the light switch off behind him.  Kelso waves his hand at his former co-workers and advises J.D. to get as much tail as possible before taking off.  Elliot suggests to J.D. that if he really wants them, he should ask people for his goodbyes.
Just a Day
Heeding her advice, J.D. approaches Cox, explaining that he wants something from his mentor.  Dr. Cox searches through his book of rants, but can’t find one to combat J.D.’s desire for attention, so he decides to create a new one.  Cox understands that J.D. wants him to recognize that this is a special day, but getting emotional has never been his MO.  He tells J.D. that today is not a special day for him, it is just a day.  J.D. tells Dr. Cox that if he decides to add that speech to the book he made, he should put the number five next to it.
Carla assures J.D. that if he waits it out, Cox will eventually crumble and confess his sorrow at the fact that J.D. is leaving.  J.D. asks Carla why she never tortured him when he was new.  Carla tells him that “Bambi” needed a teacher.  Bambi thanks Carla, and asks if he can do anything to repay her.
“Tell me my husband loves me more than he loves you,” she demands.
“It’s about the same,” J.D. replies.
“I’ll take it.”
The Truth Will Set You Free
Turk approaches J.D. in the hall and apologizes because he feels as though he said his goodbye too early.  They hug and J.D. remarks that Turk smells like regret.  After going his own separate way, J.D. runs into Janitor who has blackmailed Denise into acting out a scenario which closely resembles the whole penny scenario from J.D.’s first day.  Denise has been made to confess her treachery, and Janitor gives her ten dollars, showing J.D. that if he would only confess, he might bridge the gap between himself and his tormentor.  J.D. finally admits that the penny had been his, but that the whole thing had been an accident.  He had dropped the penny and it had rolled under the door.  It was his first day, so he didn’t want to be responsible for jamming the door and looking like an idiot.
J.D. is surprised when Janitor tells him that he knew the penny had been his all along.  In fact, Janitor had seen the whole thing.  J.D. asks why Janitor has been pestering him for the truth if he had been a witness from the beginning.& nbsp; Janitor says that he wanted J.D. to admit it; the query had been a test of character.
“You failed,” Janitor adds.  He also explains that in failing, J.D. missed out on what could have been a great friendship.  Janitor turns and walks down the hall.  J.D. asks if he wants to be friends starting now.  In response, Janitor pauses mid-gait, seems to think, but keeps on walking away.
Moment of Weakness

Jordan retracts her claws for a moment to say goodbye to J.D. who is touched by her words.  Her moment of weakness leaves her feeling like she needs to pick on someone.  She calls to Ted, explaining her need to make someone feel bad.  Ted actually comes to her, and he helps her pick on hi mself.
J.D. takes a step back to analyze the place that has been his home for so long.  He realizes that Cox is always going to be a gruff, insensitive teacher, and J.D. should be grateful that the man had been his mentor.  He also wonders if he’ll see his buddy Turk as often, if he’ll stay with Elliot, or if Cox will miss him when he’s gone.  He finds a moment to ask Dan why he won’t take the test.  Dan says that if he takes the test and finds out that the disease will eventually kill him it will be knowledge that he can never unlearn.  If he doesn’t take the test his future will be undetermined, and that means it’ll still be his.  If his future is undetermined, it can be whatever he wants it to be.  J.D. gets exactly what Dan is talking about.
J.D. sets down his last chart and the Janitor approaches to say his farewell.  J.D. begs Janitor to finally reveal his name.  Without missing a beat, Janitor tells J.D. that his name is Glenn Matthews.  J.D. is surprised that Janitor would confess his name that quickly, and Janitor asks him why he is so surprised: it was the first time he ever asked!  It seems that being able to give his enemy a name smoothes over the years of indignation either has suffered from the other.  J.D. walks off happy.  A doctor approaching from the other direction waves at Janitor and calls: “Hey Tommy!” proving that nothing has changed.
Collecting What’s Owed
Cox and Sonny stand over a patient and J.D. ducks his head in the door to say goodnight.  Cox nonchalantly throws a “goodnight” back over his shoulder and J.D. leaves.  Sonny looks up at Cox and says that J.D. is being a little ridiculous… making a big deal over nothing.  After all, he’s a good doctor, but there’s nothing special about him.
The look on Cox’s face grows stern and his cold eyes meet Sonny’s.  In Cox’s final rant, we learn how he truly feels about Doctor John Dorian.
“J.D. is not only an exceptional doctor: he is a damn exceptional person.  That’s why people gravitate towards him.  That’s why I gravitate towards him.”
Meanwhile, J.D. has snuck up behind his mentor, soaking up his words like rays of God’s sunlight.
“Thank God!” J.D. exclaims, once Cox has finished speaking.
Cox shudders, and grits his teeth, realizing that he’s been busted.  When he turns J.D. goes in for the hug, and a begrudging Cox finally gives it to him.
“You smell like a father figure,” J.D. whispers.
J.D. thanks Sonny for delivering her lines correctly and cheers his way out the door.  Cox points out to Sonny that even though J.D. is leaving, she still has to work there.  Sonny realizes that she didn’t really think that one out, and Cox agrees.
How it Ends Here
J.D. doesn’t realize why he cares so much about how it ends for him at Sacred Heart.  What should matter most is that he changed lives within these walls.  As he walks through the halls he runs into the people who made an impact in his life.  Todd gets one last h igh-five, and his brother Dan stops him to say goodbye.  A few of the girls he’s dated walk through the halls to smile at him one last time.  When he reaches the last strip of hallway everyone is there to see him out, even some of Sacred Heart’s ghosts.  Laverne smiles at him, as do some of the other patients who died under his care.  They all show up to see him off in what J.D. perfectly describes as “a wave of shared experience.”  Turk, Elliot, Carla, Cox, Janitor, Ted, Todd, Jordan, Dr. Mickhead, Doug, Keith… they all form a gauntlet for J.D. to pass through on his way out the door.  He realizes that even though this place was warm for him, he knows it has to end.  When he reaches the door, J.D. turns one more time to look back at them, but they are gone.  They hadn’t really been there… but then again, they had been there all along.  Before pushing through the door, he resolves that one should live in the past for too long.

Recap by Jonathan Friedler