Season Premiere. The ER treats victims of a gang shootout. Carter arrives late and unprepared for his new position. Mark learns all about being an attending, including senior staff's habit of bad-mouthing the residents, particularly Doug Ross. Mark hires a new chief resident, Kerry Weaver, and new third year med students arrive to complete their ER rotation.
Weaver manages to offend just about everyone on her first day as chief resident. Carol goes on a ride-along with paramedics Shep and Raul, and later shares a ferris wheel ride with Shep. Benton and Jeanie's secret relationship comes to a head. Susan is stuck caring for Little Susie while Chloe attends school. Doug has his hands full with a young pyromaniac. Carter shows interest in med student Harper Tracy.
Carter gets his first patient, and loses him. Susan's feud with Weaver intensifies when she demands all of Susan's procedures be cleared with her. Chloe abandons Little Susie again for a lucrative career in the flea market business. Carol finishes her paramedic recertification by picking up a very overweight, lethargic man, after which Shep hits on her. Jeanie ends her relationship with Benton. Wendy conducts interviews with various ER staffers for an article on Mark. Doug cares for a four-year-old Asian boy with AIDS.
Weaver and Susan's feud escalates to the point where Mark has to step in. Benton is involved in a parking lot altercation, resulting in a dislocated finger and Carter replacing him in surgery. Mark cares for an abandoned elderly woman. Susan tries to juggle her work and care for Little Susie. Shep risks his life to bring in a gunshot victim.
Doug treats the dying Chia-Chia. Susan tries to find a way to keep Little Susie, asking her parents for help. Benton treats an injured woman who refuses to press charges against her abusive policeman husband. Carol and Harper are tricked by a patient from the "turkey file." Lydia helps Loretta the prostitute outfit herself for a job interview. The staff celebrates Weaver's day off.
Speculation runs through the ER, on a very hectic day, about Randi's possible criminal history. Mark faces an ethical dilemma when he has to decide whether to report yet another of Doug's indiscretions; he slept with med student Harper Tracy. Carter becomes upset when she confesses this to him. Carol meets with a mobile notary to finish the paperwork to purchase a house. Bernstein informs Doug that he needs to look for other employment. Benton is visibly upset when Jeanie begins work in the ER as a physician's assistant.
Doug decides to leave County and accepts a well-paying position in a private pediatric practice. While on his way to a fundraiser after his last ER shift, he gets a flat tire during a torrential downpour. A young boy finds him in his disabled car and asks him to rescue his 12-year-old brother, trapped in a nearby flooded culvert. Doug is able to get the boy out, but must improvise further in order to keep him alive. Back at County, Benton, Carter, and Harper work hard to save a young hit-and-run victim whose bickering parents further complicate the situation.
Doug's heroics earn him a second chance as Bernstein and Morgenstern ask him to stay on. Doug and Mark clash when each treats a seriously injured patient and want to use the same equipment. Benton learns that Jeanie has separated from Al. After missing an earlier diagnosis, Carter overcompensates on his next patient and catches a break when the test results reveal something. Shep gets on Carol's bad side when he makes disparaging remarks about people with botched suicide attempts. Doug gets a phone call from his estranged father. Later Doug shows up drunk for his own awards ceremony threatening an obnoxious speech, but he reconsiders and recovers nicely.
Carol and Jeanie try to find a home for a schizophrenic architect. Carter signs Benton up for an interview with Vucelich for a prestigious study. Carter and Harper try to find a place to make out, after which he spends the day with a bandage on his neck to hide the hickey. Jenn and Rachel are involved in a car accident. Meanwhile, Mark is thrown for a loop when he learns that Jenn has been having an affair with a co-worker. Doug dines with his mother. Susan receives 00 in the mail from Chloe.
The ER staffers are in decidedly unfestive moods as Christmas arrives. Carol's spirits are lifted by a Santa-like patient. Mark is outraged when Jenn decides to stay in Dayton over Christmas. Benton and Carter score points with Vucelich when Carter convinces an older gentleman, Jules "Ruby" Rubadoux, to include his wife in Vucelich's study. Mark gives a deposition in the O'Brien case. The death of a priest threatens to start a gang war. Weaver receives a surprise visit from an African friend. A Holocaust survivor, the victim of a carjacking, brings Chanukah to the ER.
Shep and Raul bring a dozen malnourished and abandoned children into the ER, keeping everyone very busy. Shep has a run-in with Malik and Benton when he makes an off-handed racially insensitive remark. Carter's high from the admission of Mrs. Rubadoux to the study ends when she shows no signs of recovery. Jeanie and Carol clash when Jeanie receives a poor evaluation. Al asks Jeanie to give him another chance. Mark is served with divorce papers.
Mark tries to find a way to tell Rachel about his impending divorce. Benton attends a banquet at Vucelich's home, with Jeanie as his date. Carter finally tells Mr. Rubadoux about his wife's terminal condition, making the man furious. Morgenstern is admitted to the hospital after breaking a leg at a Scottish family reunion.
Mark is riddled with self doubt as the hospital prepares to settle the O'Brien suit. Weaver appoints herself as Susan's personal mentor. Carol minds a bucketful of expensive worms. Doug balks at counseling a teenage boy who thinks he might be gay. Benton uncovers some disturbing information concerning Vucelich's study. Carter steals a diagnosis from Harper.
Benton decides to blow the whistle on Vucelich's unethical study methods, causing Vucelich to drop him from the study. Susan treats a street couple, one of whom has passed HIV to the other. Doug receives a visit from his estranged father. Carter spreads rumors about an affair between Mark and Susan. Mark buys a motorcycle. Mark tells Loretta that she has cervical cancer. Carter shows up at Ruby's late wife's funeral. Ruby was not impressed.
The ER hosts roughly a dozen pregnant women when a sprinkler bursts in the maternity ward. Conni is past her due date for her own baby. The ER gang try to convince her that the beet soup at Doc Magoo's will help her go into labor. Carter plays tour guide for the visiting surgical intern hopefuls before going through the interview himself. Benton tries to bring a hopeless patient back from the brink of death in a marathon surgery. Jerry tries to convince the others that basketball player Scottie Pippen visited. Doug visits his father.
Shep and Raul respond to a massive fire without proper equipment, risking their lives to save addicts and their children. Shep will be okay, but Raul has third-degree burns covering his body; it's only a matter of time. The ER is flooded with burn victims. Chloe returns to Chicago. Doug is stood up by his father for a basketball game.
Susan institutes extra precautions in case Chloe tries to reclaim Little Susie. Mark changes his look, growing a goatee and wearing contact lenses. Carol and Jeanie square off over the care of a transient. Carter celebrates when he receives his residency match, putting his patient and his job at risk. Shep, still suffering from Raul's death, is surly with new partner Reilly. Benton and Doug have differences when Peter discloses a critical mistake made by Doug, raising animosity between the two.
Mark finds himself staffing a very crowded ER on his scheduled night off, filling in while Doug is out with whiplash and Susan meets with her lawyer. He tries to juggle hunger pangs, 40+ patients in the waiting room, and a never-ending stream of traumas.
Carter engages in competition with new surgical resident-in-training Dale Edson upon learning that residents will be evaluated and graded, with only the top ones advancing to second year. It doesn't help that Dale once had a relationship with Harper. Mark flirts with infomercial director Iris, and a hidden camera captures some private conversations. Benton faces the fallout from his altercation with Doug when surgeons begin dropping him from procedures. Shep begins exhibiting uncontrolled hostility, first to a patient being abusive with Carol, then a pedestrian. Susan and Chloe try to reach an agreement regarding Little Susie.
Susan throws herself into her work to escape her stressful personal life, earning recognition from Weaver and Mark, who begin preliminary discussions on next year's chief resident. Carter needs a pediatric rotation with Doug, and fast, to graduate med school. Doug takes up with his father's girlfriend. Shep overreacts and attacks an Asian boy interfering at a scene. Mark and Jenn try to discuss their divorce amicably, with unforeseen results. Benton is named Resident of the Year. Harper leaves for an OB rotation at Parkland in Dallas.
Susan consults a therapist to cope with the loss of Little Susie. Jeanie's estranged husband Al checks into the ER complaining of flu-like symptoms, which turn out to be caused by HIV. Shep expects Carol to back his version of events during an official investigation of his behavior. Loretta takes a turn for the worse. Doug discovers that his father has disappeared with a lot of Karen's money.
Season Finale. Carol is pushed to the breaking point after another day when politics triumph over health care, and she quits. Mark "trades his soul" when he agrees to back Weaver for ER attending, in exchange for her support of Susan for chief resident. Jeanie takes an HIV test and informs Benton he should get himself tested as well. Carter invites Benton to his med school graduation, which he himself misses in order to keep a young patient company. Shep's refusal to see a psychiatrist risks his relationship with Carol.