Season Premiere: Carter returns from Africa, going straight to Abby's bedside. Her response to seeing him is to ask for her key back. She is very chilly towards him all day until new med student Neela Rasgotra answers a phone call for Carter. The message: Luka is dead. Carter decides to go back to the Congo to bring the body back. Abby pleads with him to stay, but he leaves anyway. Neela has a tough first day in the ER, earning Chen's ire after Pratt flirts with her. Gallant, now a full-fledged doctor, helps to show her the ropes. Romano returns from his medical leave. Susan is still seeing Chuck. The ER is being rennovated, causing Weaver to scream a lot.
Believing Luka is dead, Carter returns to the Congo. There, he learns about Lukas fate from Charles and Gillian, and begins his search for Lukas body. In flashbacks, we see Luka from the time Carter left 22 days earlier. Still at the Matenda clinic and under threat, Luka contracts malaria as he cares for his remaining patients. He, Patrique, Chance and her mother and are soon captured by Mai Mai, and held with a group of prisoners the Mai-Mai execute. With the help of Debbie, a Red Cross worker, Carter and Gillian find their way to where the bodies from Matenda are kept, but Lukas is not among them. They learn one man, a priest is still alive, and discover it's Luka. As the flashbacks continue, we see that a cross given to Luka by Chances mother along with Lukas prayers lead the Mai-Mai to believe he is a priest, which saves his life. Carter, Debbie and Gillian find Luka in a compound nearby, close to death. Gillian accompanies Luka on a plane home to Chicago. Carter decides to remain, giving Luka a letter to take to Abby.
New residents arrive at County, including 2nd year Nick "Coop" Cooper. Coop talks back to Romano and is nearly killed when Neela gives him too much epi during an asthma attack. Pratt and Chen's dinner is invaded by her parents. Chen later dumps him when he states his feelings about their relationship. Romano's hospital insurance doesn't cover a good prosthetic arm. Instead, he gets a hook. He has been trying to cut the budget by giving the nurses fewer shifts and filling the rest with temps. Most of the nurses stage a walk out and receive 90-day suspensions as a result. Abby and Lewis treat a girl whose parents don't want to tell her that she's dying. Fast Eddie and Corday do it in a car. Luka arrives at County and Gillian gives Abby her letter from Carter, in which he dumps her. Frank picks it up off the ground from next to a trash can and soon everybody knows.
Pratt is left in charge of a busy night shift, with only a few med students and fellow 2nd year resident Dr. Coop. Both Neela and Pratt make mistakes with their patients. Abby is looking for a loan for a secret endeavor; she finally gives in and begs her ex-husband to co-sign. Romano gets his Utah arm. Abby visits Luka, finding Gillian in the middle of saying goodbye. Corday and Dorset are still doing it, although Corday wonders if it's too soon after Mark's death.
Luka's first day back in the ER is a busy one. While working out the details of his return with Weaver, he mentions that he'll be returning to the Congo in two months. Lewis treats an alcoholic mother who set herself on fire in front of her son, and an elderly architect who tried to commit suicide because he's going blind. Abby appears as a surgical consult as she's back in med school. Sam Taggart replaces her on the nursing staff. Dorset's wife calls while he's in surgery with Corday.
Since his return to County, Luka has become obsessed with treating and streeting patients as quickly as possible. He argues with Pratt over the treatment of a pregnant woman who doesn't want her premature baby to receive life-saving treatment, as well as with Romano, who wants more tests ordered on patients so that the hospital can make some money. Abby is still on her surgical rotation and Romano is still riding her hard. Coop flirts with Chen. Susan has been reading to Ben Hollander in her spare time and he seems to have developed a crush on her. Luka meets Sam's son Alex in the new JumboMart (which has replaced the fire-damaged Doc Magoo's).
Lewis has a rough day: Chuck proposes having kids with her, she misses an appointment with an auditor, and Ben Hollander commits suicide. Pratt receives an unfavorable review from Romano and also treats a con who was raped in prison. Abby, on her ER rotation, agrees to study with Neela. Gallant makes a decision that results in the death of a young girl with leukemia. Sam's son Alex spends the day in the ER, following Luka around for most of it, ending with Luka X-raying his head. Chen gets a call from the Chinese embassy and heads for a plane as her vacationing parents were in an accident. Sam unscrews Romano's hand and Lewis locks it up for the rest of the shift.
A helicopter crashes on the roof, falling into the ambulance bay where it lands on Romano and causes a huge explosion. Pratt and Morris are pretty lucky: Romano had just fired Pratt and caught Morris smoking weed in the ambulance bay. Susan worries that Chuck was onboard, although it turns out he wasn't, even though he does have some internal injuries, which he will recover from. Abby daydreams about what Carter's up to in Africa. Luka enjoys Thanksgiving dinner with Sam and her son Alex.
Gallant's sister is in town and Pratt hits it off with her. Corday is the only one that attends Romano's memorial service. Alex steals a severed finger and later goes missing, turning up at County to see Luka. Luka and Sam share a moment. Neela treats two Amish kids who were injured on a sojourn into the city.
What has Carter been up to for the past seven months? He's been in the Congo developing a relationship with Makemba "Kem" Likasu, an AIDS-clinic worker, who is six weeks pregnant with his child. Carter needs to return to Chicago to take care of his grandmother's estate, so he talks Kem into going with him to have the baby in Chicago.
Carter is back in Chicago with Kem in tow. His return to the hospital is uneventful, although there is an awkward moment when Kem meets Abby. Sam gets called to Alex's school as it seems that he was suturing his own cut. She asks Abby whether the nurses' insurance covers family therapy. Gallant discovers that his sister has been getting it on with Pratt, although she later dumps him. Pratt accidentally breaks a patient's neck while doing an unsupervised intubation. Missing Valium is found in Weaver's labcoat, although it's implied that Morris took it. Luka informs Weaver that he's leaving for the Congo in two weeks. However, he later decides to stay in Chicago indefinitely.
Abby and Neela spend 21 days on their NICU rotation. Parents of twins return to China with only their healthy son. Another couple spends 21 days in the NICU before finding out their son will die. Abby and Carter discuss his impending fatherhood. Weaver and Sandy have a baby boy.
Kem accompanies Carter to work and manages to annoy about half the hospital over the course of the day. Weaver has used the money that Romano left to the hospital and unveils the Robert Romano Center for Gay, Lesbian, Bi and Transgendered Health Care. Gallant is doing a ride-along with Morales and Bardelli. Weaver offers Lewis the acting ER chief job, but Susan refuses because she's pregnant. Pratt is questioning his abilities as a doctor. Chen calls the ER to tell Pratt that her mom has died in China. Sam finds out about Luka's reputation as the ER bed hopper, but finds herself making out with him by the end of the day.
Sam treats a mother whose family was in a car accident and a 16-year-old pregnant girl whose boyfriend loaned her out to his friends. With Alex at a sleepover, she gets lonely and heads over to Luka's, where they consummate their relationship. Carter shows Kem the city and proposes they move into a townhouse he bought for them, but she leaves to go back to Africa for a while. A Human Resources consultant is sent to the ER to observe the staff. Morris chokes on a french fry and Sam performs the Heimlich on him.
An entire family suffering from carbon monoxide poisoning is brought to the ER. Claustrophobic Neela must spend a couple of hours in a hyperbaric chamber with the family's newborn baby. Carter misses Kem, who's been gone for a month now, so Jerry arranges a webcam chat for them. Luka and Sam have been keeping their relationship a secret from Alex, although he finds out and isn't too thrilled about it. After Sam suggests they take their relationship slower, Luka isn't too thrilled either. Dr. Lawson asks Elizabeth out. Sandy's mom brings Weaver's son Henry in. Chen returns from China: her dad needs 24 hour nursing care and she's having trouble getting adjusted to that idea. Susan and Chuck visit her dad and tell him about the pregnancy.
Morris streets a patient without getting a psych consult. The patient ends up stealing a tank and heading for County. Gillian visits Luka, and Sam is not happy about it; the two make up by the end of the day. A 13-year-old boy comes in with chlamydia. Frank has a heart attack, and his wife shows up with their Down Syndrome daughter. Corday plays the dating game, going out with two men.
Carter sticks up for Neela when the other attendings doubt her future in the ER. Neela caves to the pressure and accidentally gives a patient the wrong medication, however, Gallant takes the blame. Sam and Luka try to plan Alex's birthday party. Frank visits on his way to therapy. Chen's home nurse quits after her dad behaves poorly. Chuck rumbles with a man who wants to feel Susan's pregnant belly. A flasher gets beat-up by Catholic school girls twice.
Sandy Lopez dies after going into a fire in an abandoned warehouse. Kerry is devastated; even more so when Sandy's family won't let her see Henry. Susan and Risk Management interview everybody who was involved in last week's death. Gallant reveals that the Army is sending him to Iraq and he and Neela share a bittersweet farewell. Sam is surprised by the arrival of Alex's dad. Neela passed her boards, although Abby did not. Corday discovers that she's the new Head of Surgery. After she has contractions, Susan is put on bed rest for the rest of her pregnancy -- five weeks.
A patient accuses Pratt of paying too much attention while giving her a breast exam and later demonstates his technique on Jerry. Luka seems okay with Alex's father hanging around. Abby's on her psych rotation, while Neela begins her research rotation. Chen's dad is admitted to the hospital. Weaver is granted custody of Henry for the weekend. Corday is uncomfortable when Dave and Dr. Lawson meet. Abby discovers that Carter paid her med school tuition.
Still on her psych rotation, Abby treats a young mother who's having seizures caused by bad memories of her young son who died eight years earlier. Later, she takes her boards again. Weaver considers leaving town with Henry. Neela saves the life of one of her fellow researchers. Kem returns to Chicago, just in time for a Carter Foundation board meeting. Carter announces that the business will be switching focuses from arts & entertainment to medicine. His father and other board members are not pleased.
Carter notices that the baby is not kicking. A visit to the hospital reveals he has died in utero, and labor must be induced. 19 members of Neela's family are coming into town for her graduation. Abby, Neela and Lester graduate from medical school. Steve continues his efforts to get Sam back, visiting Luka at work and sending Sam a box of ice cream sundaes. Pratt refuses to believe that a patient of his is in congestive heart failure. Weaver suggests to Abby that she will match at County, unless she fails her boards. Rachel Greene is in town "looking at colleges," although she has a favor to ask of Corday.
Season Finale: Good samaritan Luka stops to help a woman with a dead battery, and comes to her aid when she is hit by a reckless driver. Abby discovers that she passed her boards. Pratt is concerned about Chen when she comes to work with a black eye. Neela withdraws from her residency program at the University of Michigan, knowing that she can't be licensed without an internship. When Steve announces his intentions to stay in Chicago, Sam hurriedly leaves town despite Luka's attempts to stop her. The custody battle for Henry Lopez goes before a judge. While Pratt drives Elgin Gibbs home en route to dinner with Chen, the three are shot at by an irritated driver.