The new chief of medicine (Courtney Cox) arrives and fires the Janitor. Dr Cox is convinced she is a jerk and eventually is proven right. JD is struggling with his new interns because of their bad attitude and behaviour. Elliott is worried when her friends tell her she has been self absorbed and whiny.

JD and Turk give up on their special steak night to comfort a dying patient.

Carla takes Katie aside and tells her not to make everyone hate her. Dr Maddox is so vigilant that no one can work the system and treat their patients. Dr Cox goes to Dr Kelso to get help and the board fires Maddox.

JD and Elliott are getting closer and decide to get back together. Dr Kelso realises he has more time on his hands than he had thought but decides he doesn’t care if people think its sad that he still hangs out near the hospital. The Janitor returns and gets his job back with little effort much to Ted’s enjoyment. Turk wins Dr Cox respect.

JD, Dr Cox and Elliott choose new interns to become their personal protégé’s or lackeys. JD tries to help Denise relate better to her patients, Elliott tries to help Katie get by in a mans world and Dr Cox tries to work out why he hates Ed.

Elliott wants her first time (again) with JD to be special and with Carla away she seeks Turk’s advice. The hospital board offer the Chief of Medicine job to Dr Cox and Dr Kelso warns him what a horrible job it is much to Jordan’s anger. JD gets to know Denise better and helps her to see the strengths and weaknesses of her cold approach to patients.

Dr Cox assumes his duties as Chief of Medicine and gets advice from Dr Kelso. He finds himself besieged by employees looking for favours, paperwork and the janitor annoying him. JD needs a favour and Dr Kelso explains that he must now badger Dr Cox into doing what’s right. Meanwhile Carla helps Elliott treat the nurses with more respect.

Dr Cox tries to do it all, pick up his son, sort out the nurses schedule, take care of an old patient and teach the interns. He learns that the only way he can cope is to give some of it up. Meanwhile Ted falls for a ukulele player and can only communicate with her by singing. JD and the Janitor team up to help him out.

Carla and Turk are having their second child. No one will get excited for Turk because it isn’t their first. So he ends up lying to Ted’s new girlfriend Gooch in order to get the reaction he craves. Elliott is missing JD really badly and texts and calls him all day. She doesn’t want to end up being so dependent on him but Kelso tells her that’s what intimacy is all about. Dr Cox is confused when Carla won’t help the interns with a coma patient.

JD and Turk organise the intern’s comedy roast and end up as the butt of the joke. But they don’t let it ruin their public displays of affection. Carla manages to convince the Janitor that he didn’t see her find a hair on her boob. Interns Denise and Sunny both want to help a young girl whose mother is being overprotective. Elliott tells Denise not to in order to teach her a lesson about taking proper time away from the hospital.

Turk struggles to tell a father that his son will be paralysed. He goes against JD’s advice about not giving false hope and tries an experimental procedure. The Janitor fears that Lady is going to break up with him and Jordan finds out that Dr Cox has been wearing a wedding ring at work.

JD is getting a lot of kudos for talking Dr Cox into making positive changes in the hospital. Carla is impressed and Turk is jealous. The Janitor messes with some interns and tells Sunny that he won’t tease her because she is too weak to handle it. Denise convinces Elliott to do a biopsy on a patient and owns up when it leaves the girl with a scar. New surgical intern Derek tries not to say what he thinks about the behaviour of his co-workers.

Turk and Elliott are on call for the night shift and aim to help the interns see how far they still have to go. Howie gets the truth from a man who poisoned himself, Sunny helps a woman fart and Katie stops a man from scratching his sutures. Meanwhile Denise and Derek hook up and Elliott discovers that her patient Robyn has HIV.

The Janitor and Lady are getting married in the Bahamas. They invite everyone in the hospital but strictly for the gifts. Unfortunately JD is so touched to be invited that he drags everyone out there for a vacation. Elliott tells him that she loves him and wants him to say it back with some feeling. Turk is getting annoyed by Carla focussing all her energy on being a mum. Dr Cox teases Jordan about actually wanting to spend time with him on vacation. Ted, Todd and Kelso come along for the ride.

The Janitor and Lady get married. Jordan gives in and admits how much she likes Dr Cox. Despite their arguments Carla and Turk get to have some fun in the sea after all. JD tells Elliot he loves her in the nicest way he can think of.

JD and Elliot drive baby Sam back to Kim’s. There they meet Sean and find out that their two exes are now a couple. The four air out all the tension between them and JD decides he wants to move closer to his son. Dr Cox has to name a new Chief of Surgery and everyone thinks it should be Turk. But Cox doesn’t like him and has to be talked into it by Kelso who is convalescing at Sacred Heart and misses being a doctor.

JD gets a new job at a hospital near his new home. He and Turk argue over a patient but really they are just sad to be losing one another. Denise is struggling and making mistakes and Elliot decides to shield her from some of the responsibility. Dr Cox isn’t happy about that but again he is really upset about JD leaving. Ted and Gooch are moving in together and Dr Kelso thinks about going back to work. The Janitor is not happy with everyone changing, including Lady asking if her sister and her son can move in with them.

It’s JD’s last day at Sacred Heart and he is thinking about his first. He becomes sad when only Turk and Elliot seem to care that he is leaving. The Janitor quizzes him about the penny he thinks that JD put in the front door eight years ago. Dr Kelso starts work again, steals his favourite table from the Coffee Bucks and says goodbye to JD. Dr Cox refuses to give JD the goodbye he wants. JD diagnoses a lady with Huntington’s disease and has to tell her son that he may have it too.

JD says goodbye to Carla, Jordan and the Janitor. Elliot admits she has moved in with JD. Sunny tricks Dr Cox into finally revealing his true feelings about JD as JD listens. Through his Huntington’s patient and her son, he sees that his future is whatever he can make of it. He remembers all the faces that had an impact on him while at Sacred Heart. Then he imagines his future and leaves.