Season Premiere. Carter begins the first day of his internship with the difficult task of filling in for Benton as the ER surgery consult. Haleh and the other frustrated nurses teach Carter a lesson. Jeanie makes a difficult decision regarding her HIV-positive status, while Benton's test comes back negative. The ER staff is buzzing regarding a rumor that a Chicago hospital may be closing. Weaver implements an incoherent system for tracking patients. The ER staff plays in a Fourth of July softball game, where Carol runs into Shep and his new girlfriend. Benton runs into an old friend, Carla Reese, at Jackie and Walt's barbecue.
Jeanie begins to realize the burden of living an HIV-positive life when bills start mounting up and Benton throws her out of a trauma. The staff nervously awaits news on the hospital's future when it's rumored to be closing. As it turns out, Southside is closed instead, and County takes on a new chief of staff, Dr. Anspaugh. Mark and Susan endure disastrous blind dates. Benton sends Carter to the ER for the day after he arrives late. Carter then talks a patient into a local anesthetic and encourages him to ask Benton questions during the operation.
Mark is befuddled by an invitation from Susan to go on a joint vacation to Hawaii. The ER is filled with more refugees from Southside, Drs. Maggie Doyle and Abby Keaton among them. Benton decides to join Keaton's pediatric surgery team. Carter gets on Anspaugh's bad side when he exaggerates a patient's condition to book an operating room. Jeanie tries to keep her HIV status a secret in the face of Weaver's queries. Jerry tries to trap a loose kangaroo. Mark spends his entire day working on one patient, against Anspaugh's decree that ER attendings and residents should handle 2.5 patients per hour. Carter's apartment building burns down.
Doug brings a one-night-stand into the hospital when she has an epileptic seizure, earning him the stares of his colleagues when he can't remember her name. Carter screws up Benton's lecture when he realizes Benton's presentation materials were destroyed in his apartment building's fire. Keaton takes a shine to Carter, meanwhile, when he persuades a teenage girl to undergo surgery. Carter also finds a place to live, with Dennis Gant. Jeanie begins experiencing side effects from her medication and is asked out by a handsome construction worker. Carol ponders enrolling in med school.
Doug and Carol man the Healthmobile, a roving medical van that caters to the homeless. Benton tries to be more warm and friendly towards children, even taking a group of hospitalized youngsters trick-or-treating, ending by standing on his head in the hallway. Gant demands more respect from Benton. Mark anxiously waits for Susan to return from vacation.
Mark and Susan take to the air for helicopter flight rotation, which brings to the ER an entire family injured in an accident. Benton's overconfidence during Keaton's absence results in a dire mistake. Carol deals with a "floater" nurse who can't cope with the speed of the ER. Jeanie and Maggie are given the task of keeping a dead man on ice in anticipation of cryogenic storage.
Benton fights to save the life of a gangbanger already declared dead by Doug. Nurse Rhonda Sterling floats down to the ER again and makes another critical mistake. Carter fights Edson for the rights of an incompetent patient and bonds with Anspaugh in the meantime. E. Ray worries that an MRI test gave him negative karma. Carter and Keaton get closer. Mark fears Susan is dating Morgenstern; she tells him that she's moving to Phoenix.
Susan's last day in the ER finds Mark unsure of himself. Despite Doug's urgings, Mark still finds himself afraid to admit his feelings for her. He chases her all over the city until he finds her at the train station. He declares his love for her, but she decides to leave for Phoenix anyway. Grabarsky and Lydia finally get married. Carol agrees to become "management" in exchange for an end to the policy of floating ER nurses elsewhere. Al Boulet delivers divorce papers to Jeanie. Doyle calls the cops on a pregnant woman who is drunk and trying to hug her unborn baby. Charlie brings a neighbor's baby into the Healthmobile. Carla shows up in the ER and Carter gives her a tour, with Benton in tow.
Mark, still reeling from Susan's departure, crosses ethical lines to obtain Jeanie's confidential files after learning Al is HIV-positive. Benton rides Gant hard. Carter and Keaton find it harder to maintain their secret relationship, and she tells him she will be going to Pakistan soon.
Rumors sweep the ER when Kerry and Mark cloister themselves to discuss policy regarding HIV-positive employees, prompting Jeanie to publicize her condition. Charlie brings the child she has been caring for into the ER. Doug treats the child and feels obligated to report the child's mother for neglect. Doyle treats an abused woman, and conspires to help her escape her husband. Carter blows off an evening with Gant to spend the night with Keaton. Mark inherits a mangy dog from a patient and decides to give it to Rachel for Christmas, but ends up not doing so when he finds Craig has already given her a puppy. Carol and her mother host a traditional Ukrainian Christmas celebration, to which Doug shows up with Charlie, who needs a favor from Carol. Keaton tells Benton that she won't recommend him for another pediatric surgery rotation.
A long, cold night finds ER staffers with hours of time to hug. Weaver recruits staffers to participate in a study on sleep deprivation combined with physical activity. Gant appeals to Anspaugh after a public scolding from Benton. Carter ditches Dennis again to escape his whining, only to discover deadly results. Peter is denied a recommendation from Keaton one last time before she leaves for Pakistan. Mark and Chuny discover that they have a lot in common. Carol is at a crossroads when management demands she cut two RNs. Charlie comes into the ER severely beaten. Carol and Doug perform a safety check in the ER and a clock falls on Weaver's head.
Carter and Benton struggle to deal with Gant's death as speculation continues on the cause. Upset over their contract, the nurses stage a "sick-out," leaving the ER severely understaffed. Forced to work both the day and night shift alone, Carol makes a deadly mistake. Jeanie and Dr. Fischer bond while working on a patient whom they fear has a serious illness. The word is out about Mark and Chuny.
Carol takes an interest in an ailing police sergeant who's hiding a degenerative ailment. She also meets with a newspaper reporter to air the complete story on her fatal mistake and is subsequently suspended. Peter runs into a pregnant Carla, upsetting the rest of his day. Carter, already fed up with Benton's lackluster attitude, accepts a transfer to Hicks's team after Peter fails to show up at a lecture the two were to give. Jeanie and Greg Fischer disagree on whether to inform a patient's spouse that he's suffering from neurosyphilis. Weaver and Mark each take a trio of prospective students through a day in the ER, with widely differing results. Chuny and Mark break up; and both get over it rather quickly.
A gleeful Carter removes Benton's appendix. Doug treats a 17-year-old cystic fibrosis patient who wants to die, but isn't old enough to sign a DNR. Mark juggles dates with three women, including psychiatrist Nina Pomerantz. Jeanie and Greg team up to find the culprit behind a rash of staph infections. Haleh has a tough time filling Carol's shoes. Carter and Doyle have a date at the pistol range.
Carol and others, including her 10 year-old neighbor Robert, are trapped in a convenience store after a failed robbery attempt. Carol must put her medical knowledge to the test as she tries to save one of the robbers and the store's owner. The other robber is finally able to make an escape from the store, and takes Carol with him, but he is shot running away from the police.
Mark tries to get a congestive heart failure patient with Down's Syndrome on to a heart transplant list. Carter disagrees with a diagnosis by Anspaugh. Carol agonizes over whether to take the MCAT. Jad Houston turns 18 and requests that Doug take him off the respirator which has been keeping him alive. Greg and Jeanie agree to continue seeing each other.
Mark examines his prejudices when he's accused of neglecting a black gunshot victim, Kenny Law, in favor of a white victim. Jeanie discovers Benton's impending parenthood when Carla comes into the ER. Carter spends the entire day treating a hopeless case. Weaver tries to persuade a disabled junkie to enter a rehab program. Carol treats a college student who was given Rohypnol, a date rape drug, at a party the night before. After Jenn's mother has a stroke, Rachel comes to stay with Mark for a while.
Carter goes behind Anspaugh's back to get a gambler admitted for surgery, earning Anspaugh and Hicks's wrath and jeopardizing his residency. Carol clashes with Doyle, angered that a 25-year-old intern is able to order her around. Benton illegally obtains Carla's ultrasound to look for abnormalities. Doug treats an ill teenager who doesn't want to miss her prom. Mark deals with a patient who feigns symptoms because she likes having surgeries. Jeanie faces her feelings towards Al when she cares for a remorseful AIDS patient who infected her child. Jerry hits on a way to make money from a sperm bank: pass himself off as "Dr. Markovic." Rachel tells her classmates at school that she has leukemia.
Carol finds herself at a career crossroads when her MCAT results come back; she's torn between nursing and becoming a doctor, with Kerry relentlessly grooming her for medicine while Carol tries to care for a mother with a dying child. Carter debates whether to report Edson for falsifying a patient's chart. Benton takes a personal day to care for Carla. Mark treats a couple concocting odd situations to see how quickly the staff finds a solution. Jerry, Wendy, and Jeanie search for a genetically engineered mouse.
The staff springs into action when Mark is unhappyly beaten by an unknown assailant. Doug treats the son of a wealthy man, leading Carol to suspect him of giving the child special treatment. Greg demands that Jeanie choose between him and Al. Speculation runs rampant when a torrid novella, author unknown, is found at the admit desk. A new pediatrician arrives from Philadelphia. Olbes shows up out of uniform for a change, bringing in her grandfather, who has suffered a stroke. Carla is admitted to the hospital after she goes into premature labor; the contractions are stopped for now.
Mark returns to work, physically and emotionally scarred. Carla goes into labor again, about eight weeks prematurely, and delivers a baby boy. Doug thwarts Carol's efforts to celebrate her birthday quietly. Carter's doubts about whether his future lies in surgery grow. Maggie tries to interest Mark in various self-defense devices, resulting in Carter accidentally pepper-spraying himself.
Season Finale. Mark, still recovering from the attack, vents his emotions in a unhappy fit in the break room and buys a gun for protection. Carter decides his future lies in emergency medicine, not surgery, and tries to convince an irate Anspaugh likewise. There is friction between Drs. Ross and Del Amico after Doug discharges one of Anna's patients, but the two work together when a severely beaten Charlie is brought to the ER. Benton's son strengthens. Doug and Carol share a kiss. Jeanie and Al are back together.