As Residents on their first solo night shift, J.D., Turk and Elliot must work together to treat a patient. Thankfully for the patient, Carla is there to lend a hand. Cox realizes he still has feelings for his ex-wife.
J.D. inadvertently upstages Dr. Cox when he diagnoses a patient with a rare disease. Turk tells Carla that people don't always appreciate her advice. Meanwhile, a patient of Elliot's sues her for malpractice.
J.D.s mojo goes astray at the very worst time when he gets Gift Shop Girl to date him. Elliot is homeless and apparently friendless. And a pregnant Jordon takes more from Cox's offer to stay at his place then he intended.
J.D. wants to tell Elliot about his feelings, but just can't seem to find a way. Cox has to deal with a man who comes to the hospital regularly, always thinking he has something new wrong with his health.
J.D. discusses the philosophy of death with a transplant patient. Elliot feels that having a unisex locker room at the hospital is unfair. Meanwhile, Turk proposes to Carla just before she leaves for 5 days to take care of her grieving mother, leaving him to ponder over what her answer will be.
Janitor and his colleagues are assigned the task of "taking care of" J.D. but not for long. Jordan comes in to the hospital for her Ultrasound to reveal the sex of the baby. Turk's recently divorced brother comes to stay for the weekend. Meanwhile, an old friend of Kelso, Dr Townhend (Dick Van Dyke) puts a patient's life in jeopardy, causing Kelso to question his obsolete methods as a doctor.
Where Perry talks to his psychiatrist about how Jordan wanted him to bond with her family but instead he preferred to stay home and invite some of the guys at the hospital to his place to watch a game, JD gives him the advice to give Kelso the check-up that the later needs for his insurance and Perry actually listens.
J.D. and Turk play golf on the roof and apparently cause a car accident - could karma be to blame? Jordan reveals a life altering secret to J.D. on the day of the birth of her baby. Carla goes a little more crazy.
JD meets a Dr. that used to be a residence under Cox and he takes his advice on how to deal with Dr. Cox and eventually finds out that the reason Cox hates that Dr. is because he slept with Jordan and that's why they got divorced. While Carla feels that she is not sexy anymore and finds out that it's because she's engaged.
Perry is jealous from the baby taking the attention of Jordan, Elliot tries to sabotage her relation with Paul, Turk and Carla are arguing more after they got engaged, in the middle of all this mess JD feels lonely and starts a weird relation with TCW which stands for Tasty Coma Wife, a wife of a patient in coma that starts to feel alone so goes out with JD but then they decide that she needs to take more time.
JD is to start his surgical practice and he would do anything to be in the group, and anything DOES include selling his best friend. Perry -frustrated by the crappy computers Kelso gives them in order to buy fancy stuff for himself- takes advantage of Kelso being away and starts a rumor that Kelso died which makes everyone happy.
JD is dating TCW but he finds out that she is a drama queen, just like Elliot told him. Refusing to admit to Elliot that she was right, he tries to keep the heat in his relation. Carla's mother dies while Carla is planning for the wedding. Overthrown by emotions, she decides to get married as soon as possible in a small wedding chapel in the hospital. Kelso makes the interns that mistreat patients take seminars from him to avoid lawsuits. When doctor Cox is witnessed harassing a patient, he gets stuck with organizing the seminars.
It's the end of their 2nd year and everything starts to feel boring, but they have their college pal to cheer them up, and get them into trouble. Dr. Kelso is on his annual "picking somebody to pick on so that everybody will be scared of him", he picks up Elliot for almost blinding him, almost gets her to quit. Perry discovers that he is the father of Jordan's child, he gets angry and tries to break up with Jordan but she won't let it happen ,then he tells JD that he is not mad at Jordan but he is actually scared from the idea of being a father.