A run in with her old flame Sean and an accident in her new car leads Elliot to the realization that nothing good has happened to her in the three years that she has been at Sacred Heart, driving her to take drastic measures, including a complete makeover, both inside and out in an attempt to change her luck. Meanwhile, JD gets stuck with a patient whose diagnosis he can't quite pin down and when Dr. Cox denies him any assistance, he looks to Carla and Turk to help him out. While Dr. Cox is busy not helping J.D., he takes the time to make amends with Dr. Kelso.

When Carla and Turk set the date for the wedding, JD realizes this is the end of an era in their friendship, but his efforts to celebrate this milestone are rebuffed by Turk. Elliot is determined to win back her old boyfriend Sean, but is again faced with tough choices between a relationship and her career.

As third year residents JD, Turk and Elliot get their own set of interns and realize that they each have very different approaches training them. When JD needs help with training his interns he turns to Elliot and who refers him to her boyfriend, Sean who shares some of the training tips he's picked up during his time at Seaworld. At the same time, Elliot experience with her interns makes her realize that she needs to stand up to Dr. Kelso. Meanwhile, Dr. Cox and Jordan are having some trouble finding a doctor for their kid, until they meet Dr. Norris whose abrasive, yet somehow familiar personality makes his the perfect candidate for the job.

Sean is a bit surprised and disturbed to learn about Elliot and JD's history together, but it turns out his anger is really a cover up for the fact that his little work trip is actually six months long and he doesn't want Elliot to explode. J.D., who has been watching their relationship develop, finally acknowledges that he still has feelings for Elliot and that he has to come to either accept her new relationship or do something about it. Meanwhile, Dr. Cox. is forced to swallow his pride and actually ask for help when he decides to throw his hat in the ring for the Residency Director position at the hospital. Carla picks up an extra shift as a surgical nurse, which allows her to spend the day working alongside with Turk, to his great annoyance.

Dan decides to stay with J.D. for a while, since their mom's new fiance kicked him out, but after spending some quality time with him at the hospital, Dan isn't sure if he likes the cynical person his little brother has become. Meanwhile, Elliot tries to deal with her own problems of having a long distance relationship and decides to try moonlighting as a pet examiner with Carla to save up money to go visit her boyfriend as Carla saves up for her wedding.

A chance meeting in the elevator sparks a new friendship between J.D. and the mysterious Danni whose ongoing dialogue about her ex forces J.D. to talk about his feelings for Elliot. Meanwhile, Carla's brother Mark comes to visit, but things are a bit uncomfortable since he still hasn't forgiven Turk for mistaking him for a waiter at their mother's funeral. Unfortunately, Turk can't even apologize because Mark refuses to speak anything but Spanish. At the hospital, Dr. Cox is relishing his new role as Residency Director, but is a bit surprised when J.D. doesn't immediately follow his lead in contradicting Dr. Kelso's orders.

As J.D.'s relationship with Danni progresses, he and Dr. Cox are forced to spend more time together outside of the hospital, to Perry's great chagrin. However, their antics, designed to sabotage each other, end up only aggravating Jordan and Danni. Meanwhile, as they each deal with problems in their own relationships, Carla and Elliot work to find their own balance between their personal and professional relationships. Dr. Kelso accidentally punctures his eardrums giving the hospital staff an opportunity to tell him how they truly feel about him.

Turk joins J.D. in the winner's circle after he performs his first solo surgery brilliantly, leaving Elliot struggling to find her own defining moment. While the young residents wrestle with their professional challenges, Dr. Cox deals with the reality of growing older when his back goes out and he refuses to admit that he needs help. Meanwhile, J.D. gains some insight into the life of the Janitor that sheds new light on his intriguing history.

Elliot's discomfort with sex and the proper terms for the human sexual organs reaches a new high after she performs a pelvic exam on an elderly woman with surprising results. J.D.'s patient, Mr. Cantwell refuses to have surgery to prostate cancer surgery because he doesn't want to risk his sexual relationship with his wife. Meanwhile, Dr. Cox can't find the time to have a sexual relationship with Jordan and Carla surprises Turk with the news that she's decided they should abstain from sex until their wedding - a decision she ultimately reevaluates when she needs a little comforting.

Dr. Cox' disdain for Turk reaches a new high when Turk refuses to perform a liver transplant on Cox' patient after he admits to breaking the rules regarding the waiting list. Meanwhile Carla and Elliot try to make a dying patient's wish to lose her virginity come true by finding her a man -- a request that proves to be more difficult than they imagined. While the others are fighting for their patients, J.D. is blind-sided by Danni's suggestion to move in with him and he struggles to slow down their new relationship.

J.D. decides to break it off with Danni because things are moving too fast, but he dreads the idea of having to do the deed. Ultimately, he is spared when Danni beats him to the punch by having Jordan break up with him for her. Meanwhile, Dr. Cox discovers that parenting has unearthed his sensitive side and as a result, the residents don't fear him the way the used to, a situation Dr. Cox is more than happy to remedy. Elliot struggles to convince Dr. Kelso and her colleagues that her new look does not make her less of a professional.

Dr. Kevin Casey comes to Sacred Heart as a visiting medical doctor and an accomplished surgeon despite being diagnosed with a severe case of obsessive compulsive disorder. Dr. Casey touches everyone at Sacred Heart in a special way during his visit, beating his old resident buddy Dr. Cox at his own game of wits, leaving Turk in the dust with his surgery time and teaching J.D some very valuable lessons about learning to believe in himself. Meanwhile, Dr. Kelso strikes a deal with the Janitor to take care of the hospital's garbage, only to find himself eyeballs deep in it.

Elliot finds herself perplexed over a simple procedure that leaves her questioning her career path. She goes to seek Dr. Kevin Casey's advice but becomes frustrated when she learns that the epiphany toilet, which the Janitor secretly installed on the roof, is getting more attention than she is. Meanwhile, Turk asks JD to be his best man at his wedding, which sends JD into sheer bliss momentarily until he hears a phone message that makes him question his friendship with Turk.

Danni and Jordan's brother, Ben returns from traveling the world, a trip he's been on since his leukemia went into remission. When Dr. Cox learns he hasn't seen a doctor since he left, he recruits J.D to do a thorough work up. Unfortunately, forcing J.D. to drop his other patients to run tests on Ben is a decision Dr. Cox soon regrets. Meanwhile, Elliot's concern about a bunion on her foot leads to the revelation that Carla has been hiding something from Turk.

Jordan's friends Allison and Maddie come to town to provide moral support for Jordan after her brother's death -- however, their constant presence does not provide any relief to Dr. Cox. Meanwhile, Turk tries to impress the new female surgeon, Dr. Miller, but his first encounter serves only to leave him baffled by the opposite sex yet again. Attempting to reinforce the policy on sexual harassment at Sacred Heart, Carla is forced to teach a course where Dr. Kelso is the number-one student.

In a unique episode, the path of a butterfly is the deciding factor in the fate of the young doctors. At the beginning, a butterfly landing on a woman's breast sets off a chain of events ultimately resulting in the death of J.D. and Turk's patient, leaving them to wonder what they could have done to change the outcome of their day. Taking a step back in time, the butterfly takes a slightly different path, landing instead on a man's chest setting in motion an alternate chain of events that leads our characters down a very different path. Will this be enough to change the fate of their patients?

The return of Dr. Ron Ramirez to Sacred Heart from his philanthropic work abroad, sparks some doubts in Carla's mind about her feelings for Turk. When she accepts a dinner date with him, J.D. is torn between telling Turk the truth and keeping his promise to Carla. Back at the hospital, Elliot takes a stand for her patient despite the fact that Dr. Cox believes he is a drug addict faking abdominal pain to get medication. Meanwhile, the Janitor introduces J.D. and Turk to his twin brother, but they aren't buying it.

J.D is left bored after he clears his schedule to help Dr. Cox with a special project only to be pushed aside for a new intern. With some free time on his hands JD offer to help Elliot with Kids Day when she discovered she couldn't attend. His good deed does not go unnoticed, even though Sean shows up unexpectedly. Meanwhile, Turk begins to get nervous about the wedding when he has to send out the invitations. Dr. Cox and Dr. Kelso end up fighting for the attention of the new female doctor, Dr. Miller.

After an unexpected night of passion with Elliot, J.D is left frozen in shock when Sean comes back into Elliot's life. Carla and Turk try to pass on advice to J.D but despite their efforts he finds himself in bed with a reinvented Danni on the rebound. Dr. Cox is shocked by the realization that his hatred of Dr. Miller may actually be an attempt to mask a secret crush. Meanwhile, Dr. Kelso and the Janitor square off on the do's and don'ts of hospital security.

J.D. and Danni breakup again because of J.D.'s continuing feelings for Elliot. When Elliot asks Sean to move in with her, J.D. decides he has to take action. Elsewhere, Dr. Kelso and Dr. Cox face-off over whether or not the hospital should provide full body scans. As the wedding grows nearer, the pressure to make their special day perfect starts to get the best of Carla and Turk.

The eve of Carla and Turk's wedding gets off to a rocky start when Turk forgets to pick up Carla's brother Mark from the airport. The mounting pressure does nothing to help Turk as he finds himself at a loss for words while writing his own wedding vows. Another relationship seems to be in trouble as well when J.D realizes that he does not love Elliot and goes to Danni for advice on how to tell her. Meanwhile, Dr. Cox is going through fighting withdrawals when Jordan refuses to fight with him anymore and the hospital staff pays the price. Ken Jenkins and Neil Flynn also star

The day of the wedding Turk picks up an extra shift at the hospital to get some extra time off for his honeymoon. Inevitably, what should be a very simple procedure turns into a life and death situation when Turk discovers complications with his patient and he gets stuck at the hospital. Meanwhile, a very stressed out Carla tries to manage the situation at the church while her groom is missing, her brother Mark continues to antagonize her, and her guests are becoming unnerving. After telling Elliot he is not in love with her, JD tries to put together the broken pieces of their friendship by getting Sean back together with Elliot.