Season Premiere: Pratt's car crashes into the river. He and Chen are severely injured, while Elgin dies. Abby begins her internship at County, as do Ray Barnett and Howard Ritzke. Alex and Sam crash at a motel, where Alex places a collect call to Luka. Luka comes to find them and asks Sam to return to Chicago with him. The Lopez family gives Weaver full custody of Henry, and will take care of him while she is at work. Carter and Kem scatter their son's ashes. However, his proposal isn't enough to keep her in Chicago.
Carter hasn't been sleeping well, falls off the wagon, and later shows up at the hospital drunk. Luka and Sam profess their love for each other, and he invites her to move in with him. Neela's parents visit, confused by her choice to drop out of Michigan. The nurses freeze out Abby after a slip of the tongue to Haleh. Weaver advises Barnett to change his appearance. Abby treats a "damage girl."
It's a busy 4th of July. Sporting a large scar on his head, Pratt is back at work, although Carter sends him home early. Neela spends the day looking for a job, working in the Jumbo Mart across the street from the ER by the end of the day. Abby orders tests for one of Ray's patients. The new OR attending, Dr. Dubenko, declines to perform an illegal organ donation procedure between two HIV positive people. However, Carter convinces Corday to perform the operation. Luka takes Alex to his soccer game, although Alex isn't looking for a replacement for Steve. Susan, Chuck and baby Cosmo visit. New intern Howard may be obsessive compulsive.
A woman who threw her children out a third-floor window to escape their abusive father is discovered to have done it while going through Valium withdrawal. Susan becomes Chief of Emergency Medicine and discovers what it's like to be in management. Plagued by his OCD, Howard abruptly quits his internship, leaving a slot open. Susan can't find anybody to fill the position, coincidentally Neela's working across the street. Corday is in trouble after her illegal organ donation procedure, facing dismissal and loss of license. Weaver offers her a non-tenured position as a clinical instructor, but Corday decides instead to quit and return to England.
A day in the life of County's interns features Pratt ordering each doctor to discharge 25 patients by the end of their shift. Ray is quickly pushing people out the door, but may be doing it by not paying enough attention to his patients. He okays a man's organs for transplant without getting sufficient consent from the man's wife. Dubenko looks out for Abby when Ray rides all over her in a trauma. Dubenko is also a little obsessed with physics. Neela proves to be a little rusty on her first day back at the hospital.
In an episode shown in real-time, the final 44 minutes of the life of alcoholic ex-con Charlie Metcalf (Emmy winner Ray Liotta) play out as Kovac, Pratt and Sam struggle to save his life. Charlie comes to the ER with a stomach ailment that quickly grows more serious. Slowly deteriorating, he confronts a series of doctors and specialists, and the realization that he is dying. As we learn his history, he tries to connect with his estranged son. Meanwhile, Kovac confronts Pratt about his attitude, and we see how each is touched by Charlies story.
Sam and Luka move in together. When a raped and badly beaten woman is brought into the ER, Sam wants to try a risky procedure to let the woman talk. The woman dies, however, and Luka covers for Sam. At Susan's one-month review, Weaver suggests that she be more of a leader. Susan schedules a JCAHO drill, which proves to frustrate the staff more than help them learn. Even after giving birth, a young girl insists that she's not pregnant.
The 15-year-old son of a seriously wounded policeman is given the authority to decide the course of his father's treatment, and he turns to Ray for advice. Carter accompanies Wendall rock climbing. Luka begins to take a more active role in Alex's life after he's suspended for bringing a copy of Maxim Magazine to school. An exhausted Chen returns to work, where Pratt finds her stealing potassium.
Christmas Eve finds Chen unable to locate someone to cover her shift. Because she needs to care for her dad, she quits. Pratt visits her house and tries to talk her out of euthanizing her dad, but she ends up doing it anyway. Carter and Wendall share an awkward kiss. New med student Jake and Abby treat a man with lupus and a family living in their car. Carter forces Ray to miss his plane. Morris's girlfriend visits.
Susan and Abby quarrel in the ER, and an upset Abby leaves for a "smoke break" in the ambulance bay, where she is kidnapped by two gang members that want her to fix their wounded friend CJ. Abby is now faced with a life and death struggle. Back at the hospital, Susan is frustrated with her subordinates not listening to her, and faces the fact that she can't be everyones friend and boss at the same time. Susan and Luka try to teach the residents to have empathy with the patients, which turns out to be easier said then done. Wendall asks Carter out.
Weaver instructs Luka and Susan to teach the residents how to work together. Susan spends the day observing the residents, some of whom can't function under her gaze. Luka and Sam argue all day but eventually make up. Abby tells Neela that she needs to find a new living arrangement. After finding out that Ray's roommate backed out on him, Neela decides to share an apartment with him. Following another day of Luka's guidance, Neela decides that she has a crush on him. It's Abby's first day back at work since her abduction, and it may be too soon for her to return. However, after running into med student Jake on the EL (on whom she has a crush), she decides to return. Lawyer Herb Spivak returns to the ER, trolling for clients and being thrown out numerous times.
After a 16-year-old is brought in with renal failure, Carter believes that the new drug she was on was released to the public too early, causing Carter and Weaver to get into a huge shouting match. The girl's neurologist, George Henry, who recommended the drug, is a former student of Carter's. Everyone knows about Neela's crush on Luka and he tries to pass her off to Carter for the day. After Luka tells Neela that he didn't mean to mislead her, she has a brief talk with Sam about the situation. Abby and Jake work together on a number of sex-related cases. Jake wants to date Abby, but she turns him down because she obviously can't go out with her med student.
After Pratt is dumped by a woman who says he's not a grown-up, he comes to the conclusion over the course of his day that he is. He treats a young kid with a suspicious scratch on his stomach, and lets him leave before Wendall clears him. The kid is later brought back into the ER, having been beaten to death by bullies. Susan's tenure is up for review, and since she might be fired if she doesn't bring enough money into the ER, she's trying to get multiple grants. Luka and Dubenko get into a pissing contest over a patient's treatment, and Luka turns out to be right when Pratt makes a good save. With Jake off to his surgery rotation soon, he switches the remainder of his shifts with Jane so that he can work nights with Neela and be free to date Abby. At the end of the day, after Abby has finished his evaluation, he's waiting for her on her front steps.
Weaver is spending the day working in the ER when she meets her birth mother, who has disguised herself as a patient to see Kerry. Her mom is a devout Christian, in town with her choir, and does not understand Weaver's lifestyle. She offers her love, but Weaver just wants acceptance. Jake has been spending every night at Abby's apartment, which she says is for convenience's sake, but Neela thinks otherwise. Jake and Abby have trouble hiding their relationship at work, especially from Weaver. Pratt doesn't want to work with Jane. Ray gets a bedpan to the face during a fight between Carter and a Demerol junkie.
Ellie Shore is a mother of three who has a stroke and cannot speak. While she is treated, we are inside her head, hearing her thoughts. Wendall dumps Carter on their three-month anniversary, since he's clearly still attached to Kem. Neela and Ray treat three kids with a suspicious father. Morris has applied for Chief Resident. Luka and Carter want Pratt for the job, but he's not interested. Dubenko wants to write up a case with Abby, but is he interested in taking her on a date instead? Luka and Sam discuss kids.
Gallant and Neela have been exchanging letters regularly. He struggles with the war he sees every day, while she is searching for her life's purpose. He enlists her help in getting a critically burned Iraqi girl lined up for surgery in Chicago and heads for the U.S. with 72 hours leave.
Neela searches for Gallant when she discovers that he was at the hospital and didn't come see her. Eventually, he comes back and they spend the evening together. Gallant is in a hurry to leave when they visit the ER. Alex tells Sam that Steve is coming to town soon, and he actually shows up in the afternoon. Frank tells Luka that Steve is wanted in Colorado, and Luka barely talks Steve out of leaving town with Alex, who is not happy with Luka. Carter has invested money in a clinic that is more interested in glamour than medicine. Pratt hits on Olivia Evans, who works for an anti-violence organization called Ceasefire, and later winds up asking her for help with a shot kid.
Susan, Sam, and Neela treat a woman who has tried to stop her son from being deported by going on a hunger strike. Pratt struggles to find a way to convince a woman with breast cancer to seek treatment. Abby treats two elderly sisters involved in a suspicious mugging. To Weaver's delight, Carter donates 0 million to the hospital's new venture, in exchange for naming rights. After trying to connect with an icy Wendall several times over the course of the day, Carter calls Kem and asks her opinion on The Joshua Carter Center, named after their stillborn son. Morris spends the entire shift finishing-up a report for Lewis, but he keeps screwing it up. While Pratt is learning Spanish he insults a Spanish-speaking woman during childbirth by calling her a whore [Puta] starting a fight with her husband.
Jules Rubadoux, whose wife was a patient of Carter's nine years ago, comes into the ER with heart problems, wanting nothing to do with Carter, whom he feels is responsible for his wife's death. Anspaugh and Kayson advise Ruby to have surgery, but Abby tries to get him to consider the alternatives. Finally, Carter tells Ruby the truth. Pratt asks Olivia from Ceasefire out. When he shows up at her office to pick her up, he's ambushed into speaking at an anti-violence meeting. Susan meets with the tenure committee. Sam is in her own world all day, and buys a pregnancy test. Ray tries to stop the Chadwick sisters from leaving without having been seen by social services. Since there's nobody better, Morris may end up with the chief resident job.
Carter receives early tenure at Susan's expense. Luka finds Sam's pregnancy test, and discovers that she's not expecting. Pratt's friend convinces him to attend an old friend's 30th birthday party. Ray thinks a 14-year-old is a drug seeker, but he's really the victim of molestation. Abby meets Jake's extended family at his niece's baptism. Morris is named the new Chief Resident.
Carter flies to Paris to see Kem when he learns that her mother is in the hospital. Desperate to get back together with her, he offers to move back to Africa to start over again, and she doesn't really answer. In Chicago, Birdie and Rebecca are back in the ER; Rebecca was strangled by their niece Shelley, so Birdie embraced Shelley. Neela, Abby and Ray all make rookie mistakes with various patients. In therapy, Sam announces that she doesn't think she and Luka should be together. Jake indirectly tries to find out where his relationship with Abby is heading.
Season Finale: Carter's last day at County General is marked by a surprise gathering and an 11-year-old patient he delivered as a medical student. Ray is at a party and must takes charge when a balcony collapses. With all of the attendings at Carter's party, the three interns manage the traumas until Luka arrives. Pratt briefly visits his father, without revealing their connection. Upset that Sam won't let him visit Steve, whom he does not know is in jail, Alex steals Sam's credit cards and hitches a ride out of town.