On his first day at the Sacred Heart Hospital new Intern J.D realizes that being a doctor is a whole lot different and harder than he actually thought. At the end he finds out that people are not always what they seem to be at first, for example Dr Kelso who did act nice is actually a complete Jerk and mean Dr Cox is actually a good guy.
J.D, convinced that one of his patients is sick as a result of misconduct on Turk's behalf, questions not only his (Turk's) abilities as a surgeon but their friendship also. Elliot feels disrespected by Dr. Kelso after he refers to her as 'sweetheart' during rounds. In the meantime, J.D. misses his chance to kiss Elliot after being interrupted by Dr. Cox, leaving him 48 hours to get the kiss, in the fear that they will end up as just friends. Will he make it in time?
The whole crew learn their share about death when JD takes care of an old woman ready to die, Elliot and Carla watch over a woman who can't speak English, and Turk becomes too close with a patient.
While J.D. continues to misinterpret Dr. Cox, Elliot discovers parts of her body may have magical healing properties. Turk tries to woo Carla but she may not be as impressed with his gift as he thinks she should be.
J.D. is assigned to look after a difficult, but beautiful, member of Sacred Heart's Board. Her ties to the hospital may not be the only thing that makes it difficult to treat her. Meanwhile Carla freaks out after her mother in injured when she left her to spend the night with Turk.
It's Thanksgiving at Sacred Heart and J.D. is diagnosed with appendicitis. Dr. Cox tries to gain the attention of his former mentor, and former chief of medicine, Dr. Benson. Meanwhile, Elliot tries to become a 'warmer' doctor towards her patients.
J.D. and Carla struggle as cracks appear in their friendship. Turks battles Kelso for a prime lunch spot and Cox and Elliot disagree over the discharging, or not, of a patient.
It is Christmas time and no one except Turk feels like celebrating. Cox gets J.D. to video the birth of a friends baby, and once again, nothing seems to go right!
J.D. is helping Cox reach a 24hour goal without losing one patient. Trouble is, a woman slipped in the hospital and Kelso demands J.D. give her personal attention so she won't sue. Cox is also busy with his record breaking attempt to give Elliot the attention she craves.
Some pain killers have gone missing and Alex and Elliot argue over where they may have ended up. Turk discovers Cox may have inappropriate feelings for Carla.
After spending a glorious day in bed together, J.D and Elliot expect to be able to keep their new romance a secret. But this is Sacred Heart and nothing is as it seems.
Carla makes it her mission to give a coma patient his wishes. Turk tries to get J.D and Elliot back together while J.D. looks after Cox as he loses control.
J.D. struggles to treat a horrible patient. Elliot tries to confirm her suspicions that Kelso might be a rock and roll star. Cox finds himself torn between 3 women.
The parents of the interns descend on Sacred Heart. Elliot is embarrassed by hers and Turk worries over how well his Mom and Carla get on. J.D. wishes his father was more of a father.
Elliot finally has a boyfriend, but her relationship starts to get in the way of her internship. J.D. gets stuck by a needle and worries he may have contracted Hepatitis B.
When Jordan's Brother, Ben, comes in for a medical exam, Dr. Cox reveals his more compassionate side and J.D. must reluctantly deliver the bad news about Ben's health.
It is the last day of J.D., Elliot and Turks intern year. Elliot makes a big decision while everyone else tried to get a patient without insurance a life-saving operation. Jordan takes it upon herself to let everyone know exactly what has been going on this year.