Season Premiere. Benton drops Carter off at rehab in Atlanta. Three months later, a custodial strike is making life difficult in the ER. Chen discovers she is pregnant. Carter prepares to leave rehab. Benton interviews with Romano for a surgical attending position; he later gets it. Carter makes a slow journey back to Chicago, and gets busted for smoking in the aircraft lavoratory. Due to her ex-husband failing to pay her tuition, Abby cannot continue med school until the beginning of the next quarter and confronts her ex-husband at the driving range making a big scene. The ER is swamped with participants from a riot at a high school football game. Carter arrives at the ER and leaves promptly.
Domestic troubles cause problems for Greene and Corday. Later in the day, however, Mark shows Elizabeth their spacious new digs and proposes to her. Chen tells Weaver about her pregnancy; she is 22 weeks along. Carter sees Abby at an AA meeting and she tells him she was an alcoholic 5 years ago, later John asks her to be his sponsor. He also meets with Greene and Weaver about coming back to work. Abby, down from OB, helps a young couple whose baby was born much too early. Benton and Romano clash over an obnoxious homeless man who once again requires extensive treatment resulting from his chronic disdain for maintaining his dialysis appointments. Weaver and Kovac are helpless to assist a severely comatose woman whose longtime life partner is not legally empowered to make decisions on her care.
Carter treats a young paraplegic on his first day back at County. Corday and Greene try to work around a surgeon shortage. Benton discovers that Romano has fired him for his actions last week. Weaver offers Abby a position as a full-time ER nurse. Abby later plants an impromptu smooch on Kovac. Various weird patients arrive at the ER following a beam collapse at a sci-fi convention. Dr. Dave goes out of his way to discover who the father of Chen's baby is. A patient with 'spontaneous human combustion' catches fire.
Benton encounters trouble finding a new job after Romano blackballs him across town. He considers taking a job in Philadelphia, but decides to stay with County in a no-benefits job after Carla won't agree to a visitation schedule. Benton's nephew Jesse comes to the ER after getting in a fight at school. A shooting in the ER interrupts Carter's first day of treating trauma patients. Chen treats a dying young boy whose mother wants surgery for him, no matter what the outcome. Kovac and Abby go on a date, which is interrupted when they are mugged. Luka then beats the mugger to death. Greene treats beauty pageant contestants and is also enlisted by Malucci for a hockey game. Weaver treats a dementia patient who has been AWOL for 50 years.
Greene flies to Indiana to receive a heart-transplant patient. The flight back endures several problems, however. With Greene in Indiana, Weaver on her day off and Kovac missing, Romano places Benton in charge of the ER. Carter treats a teenager with HIV who has not been informed of his condition yet. Luka searches for the identity of the mugger that he killed. He and Abby later meet up in his hotel room.
Luka blows Abby off, and an already-stressed Abby has to deal with an unexpected visit from her estranged mother, who isn't taking the meds prescribed for her bipolar disorder. Corday, eager to leave work for a vacation with Greene, makes a poor surgical decision; after she leaves, her patient experiences post-surgical complications. Benton's nephew is shot and dies. Benton hears Malucci refer to his late nephew as a "banger" and Benton beats him. Chen decides to put her baby up for adoption and visits the child's father, nurse Frank Bacon. Luka accuses a pregnant girl's father of beating her.
Abby's mother decides to stay in Chicago, causing Abby even more trouble. When Weaver accepts Dr. Legaspi's dinner invitation, Weaver learns that she has misunderstood Legaspi's intentions. Carter tries to find a drug addict who has left the hospital against medical advice. Chen's mother visits the ER and invites her to dinner, even though she is surprised by Chen's pregnancy, and speechless when Chen tells her that the father is black. Greene discovers that he has a brain tumor. Corday is sued for malpractice by Mr. Patterson, the patient whose surgery she rushed so she could start her vacation, and later discovers that she's pregnant. Carter saves Abby after an explosion in exam room three.
Abby wakes up with Luka in his hotel room. At a job interview at a department store, her mother causes a disturbance and later flees town. Benton treats Jesse's girlfriend, who talks to the cops about Jesse's huggers and later comes to him for help after a hit is put on her. Corday undergoes a grueling deposition for Mr. Patterson's lawsuit and lies to save herself. Greene discovers that his tumor is inoperable and later has a seizure. He finally decides to tell Corday about his condition.
During labor Chen has second thoughts about giving her baby up for adoption, a decision complicated by the adoptive parents' presence at the hospital. With an enormous lack of sleep, Carter is called back to County to act as Chen's coach, and is later tempted to use Vicodin to take the edge off. Finch and Benton encounter trouble trying to keep Kynesha hidden from a gang. Benton comforts a little girl who is feeling used by her parents. Legaspi plants a kiss on Weaver. Greene and Corday spend the day in New York seeking help for his brain tumor. Weaver has the hiccups throughout the entire episode, trying several suggestions to stop them.
On New Year's Eve, a father injured in an auto accident is not worried about his own health, only his son's. His son is ok, but he suffers complications and requires surgery, but will be ok also. Greene undergoes experimental brain surgery in New York with Corday by his side.
Kovac treats a bishop who took a fall and questions Luka's faith. Abby pressures Carter to tell Weaver about the Vicodin he nearly took. Abby later tells him that she cannot be his sponsor anymore. After Kynesha is placed with a foster family, Benton and Finch discover their home trashed by her. Corday's malpractice suit is settled; Mr. Patterson later visits her at the hospital, causing Elizabeth to panic with another patient. Weaver and Legaspi are divided over personal and professional issues. Carter treats a woman smuggling drugs by swallowing a condom full of cocaine.
Weaver and Legaspi have spent the night together, although Kerry appears shy of beginning a relationship. She also battles Luka over calling the authorities about an illegal sweatshop employing one of his patients, which causes the owners to torch the place. Greene is back to work, but mixing up his pronouns, referring to a male patient as a "she." Corday freezes again during surgery, but is able to overcome her fears. Romano talks Benton into taking a job as County's director of diversity. In the wake of his Vicodin slip, Carter is banned from prescribing drugs. He later visits Chase at his home, and admits his addiction. Abby treats two horny old men.
Bishop Stewart returns, seeking pain medication from Luka, who also has his hands full dealing with the parents of a 16-year-old who does not want another heart transplant. Abby fills in as Carter's date for a Carter family function and sees her ex-husband there. Malucci treats a gay man who wants to contract HIV from his positive partner. Greene continues an abrupt personality change in the wake of his surgery. Weaver makes an appointment for a competency review for Mark.
Weaver spends an evening with Legaspi and her lesbian friends. Greene is furious to learn about his competency review; Corday screams at Weaver about ordering it. Chen returns from maternity leave and treats a young boy with measles. Benton struggles to get a young med student applicant an interview after learning that he was only accepted due to affirmative action. Bishop Stewart returns in even worse condition.
Carter and Luka are called out to the scene of a major train wreck, where Carter is forced to perform a double leg amputation by himself when Corday begins to experience contractions. Weaver and Legaspi treat a young, suicidal girl who caused the accident. Benton lets prospective med student William White follow him around the ER. Luka wrestles with his faith, revealing that he could have saved his wife by sacrificing his daughter. Bishop Stewart grants him absolution before his death. Also, Carter meets a new pedes intern, Rena Trujillo.
After Abby leaves the room for a second, an infant disappears from the hospital. After spending the night at her place, Carter is shocked to find out that Rena is a 19-year-old undergraduate. Greene gets his competency results--he passed (was there ever any doubt?). Malucci and Mark treat a young boy injecting steroids who is frightened of his father. Legaspi has been accused of sexual misconduct by the teenager who caused the train crash. Weaver is more concerned with hiding their relationship, so Kim dumps her.
Peter and Cleo may be at fault when a police officer shoots and kills an old woman with dementia. Carter misinforms Rena and tells her that he and Abby had a past liaison. April Fool's Day causes the staffers to play pranks on each other; Malucci gets the worst of it when Kovac injects him with Haldol, rendering him useless for the rest of the shift and getting his hand glued to his forehead while asleep. Corday endures a particularly long surgery just to prove that she can despite her pregnancy. Greene treats three young students who have been huffing carpet cleaner. Luka treats another pregnant teenager, who wants the comfort that a child will bring her.
Mark must overcome numerous obstacles, mostly weather-related, in order to get to the church to marry Elizabeth, who is stuck with both of her bickering, divorced parents. Abby has a major cold, but cannot leave the hospital, due to most of the nurses being at the wedding. Many patients come in to the ER from an accident involving a prison van; Luka and Carter clash over the treatment of an injured cop and a prisoner with a dislocated shoulder. While waiting for a flight to Vegas, Weaver (who wasn't invited to the wedding), strikes up a conversation with a friendly man. Chen misses her son. Cleo doesn't want to go to the wedding, because the bride is Peter's ex-girlfriend.
Corday goes into labor and delivers a baby girl named Ella. Benton treats his junior high school science teacher. Numerous college students come into the ER, victims of fraternity/sorority pledging pranks and hazing rituals. Carter and Abby take a road trip to Oklahoma to pick up Maggie, who has locked herself in a motel room; then she steals sleeping pills from a convenience store and attempts suicide. Rena dumps Carter over the phone.
Abby goes to court to argue for a 90-day psych hold for her mother. Her mother is released, and later shows up at Luka's hotel room. Weaver treats an old children's television show host and an animal suit fetishist. Carla checks into the hospital after a fall. Benton treats Carl Ferris again after he suffers a heart attack. Malucci clashes with Jing-Mei and Cleo when his past track record gets him in trouble. Carter treats a young girl whose boyfriend has been interfering with her pregnancy by feeding her herbal root extracts to cause a natural abortion. Chen treats a patient with a talent for numbers. Malucci calls in a priest to perform an exorcism.
Abby is flabbergasted when Maggie reveals her plans to move back to her birthplace of Minneapolis. Abby reveals to her mother that she was pregnant once, but had an abortion, scared about the genetic possibility of herself or her child turning out bipolar. Meanwhile, Carter and Chen are both shot down in their bids for chief resident, after which she tells Weaver she is a victim of discrimination. Weaver meets Legaspi's new girlfriend. Carla hits on Benton and freaks out at Cleo after she turns her back on Reese for a second and he injures himself. Mark treats a young abused boy with an extremely irate father. Most of the ER staff play in a softball game after work.
Season Finale. The father of the abused boy that Mark treated last week goes on a shooting rampage throughout the city, looking for anyone connected with the placing of his son in a foster care facility. Mark fears for Elizabeth and baby Ella's safety when Corday doesn't answer her pager. Chen moves one step closer to the chief resident position. Romano fires Legaspi. Weaver confronts Romano, and comes out to him, threatening that she will quit if Kim is not rehired. Carla's husband, Roger, accuses Benton of sleeping with Carla. Cleo cuts her hand while treating an HIV-positive patient. Luka draws unhappiness from Abby when he sends in her med school reapplication without her consent. Carter expresses his feelings to Abby and begins thinking about his future at another hospital. While treating the shooter alone in an elevator, Mark makes a critical decision regarding his care when the man flatlines.