Continuing where last season's finale left off, 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 though. Romano returns from his medical leave. Susan is still seeing Chuck. Weaver screams a lot.

Carter reunites in the Congo with Charles and Gillian. Through flashbacks, we see Luka after Carter left 22 days before. He has caught malaria, and is soon captured by Mai Mai, who begin to murder the people he's with. Gillian introduces Carter to Debbie, a worker for the Red Cross. They search for Luka, and when finally shown the body, it's not him. Carter learns that the rebels mistook Kovač for a priest and left him alive. Carter, Debbie and Gillian find Luka, nearly dead, and put him on a plane back to Chicago. Carter gives him a letter to give to Abby and the news that he's going to stick around in the Congo for a while.

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. Abby's frustrating day starts with an awful round of managing triage and gets worse when she gets a special "Dear John" letter from Carter in the Congo while her fellow nurses threaten a walkout and her opinions are ignored. Romano's mood gets nastier when he is fitted with an antiquated hook for his missing arm. Pratt uneasily meets Chen's old-fashioned parents for dinner in what turns into a last supper for their relationship.

Pratt is left in charge of a busy night shift, with only a few med students and fellow 2nd year Dr. Coop. Pratt makes a mistake with one of his patients. Abby is looking for a loan, 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 sleeping together, 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 mom who sets 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; 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, 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 riding her hard. Coop flirts with Chen. Susan has been reading to Ben Hollander in her spare time. Luka meets Sam's son Alex in the new JumboMart (which has replaced the fire-damaged Doc Magoo's).

Lewis has a rough day: 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 must gamble with a risky hospital transfer to help a young septic cancer patient. Sam's son Alex spends the day in the ER, following Luka around for most of it. Chen gets a call from the Chinese embassy and heads for a plane: her vacationing parents were in an accident.

Romano arranges a meeting with Anspaugh and Weaver to fire Pratt and catches Morris smoking weed in the ambulance bay. A helicopter crashes on the roof, falling into the ambulance bay where it lands on Romano and causes a huge explosion. Susan worries that Chuck was onboard, although it turns out he wasn't, he suffers internal injuries from debris. Abby must intubate and put in a central line without an attending. Luka has Thanksgiving dinner with Sam and her son Alex.

Gallant's sister is in town and Pratt hits it off with her. Nobody attends Romano's memorial service except for Corday. Alex steals a severed finger and later goes missing, turning up at County to see Luka. 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 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.

Carter is back in Chicago with Kem in tow. His return to the hospital is uneventful, although there is an awkward moment when Abby meets Kem. Sam gets called to Alex's school; 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 sleeping with Pratt, although she later dumps him. Pratt accidentally breaks a patient's neck while doing an unsupervised intubation. A whole nursing shift cannot go home until they find one missing Valium. Luka informs Weaver that he's leaving for the Congo in two weeks. However, he later changes his mind.

Neela and Abby face their toughest rotation ever after being assigned to the Neo-natal Intensive Care Unit, where Weaver and Sandy come needing help with their newly born son, Henry. A case involving a very ill infant tests the souls of all the doctors. Abby does well whereas Neela struggles, but both ultimately decide against going into neo-natology.

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 end up sleeping together. 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 sent to the ER observes the staff.

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 newborn baby. Carter misses Kem, who's been gone for a month now, so Jerry arranges a webcam chat for them. Alex finds out about Luka and Sam. Sam then suggests they take their relationship slower, Luka isn't too thrilled. 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, and the guy steals a tank and heads for County. Gillian is visiting Luka, and Sam's not happy about it. Frank finds himself fighting for his life after suffering a heart attack with Neela and Pratt the two unlikely doctors who successfully save Frank's life. In the process, surprising facts about Frank's life are revealed, including the deep respect he has for the colleagues he puts down on a daily basis. 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 without checking medical history. When Neela is confronted, Gallant takes the blame for her. 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.

Weaver rushes to the aid of her female partner Sandy Lopez when the firefighter is severely injured on the job and must fight for her life. Kerry is devastated 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. 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 is alarmed as he rushes his pregnant girlfriend Kem into the ER when he suspects trouble, but learns the baby died from an unforeseeable accident. Despite his own grief, Carter must help Kem say goodbye to their son after he is stillborn. Nineteen 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.

Good samaritan Luka stops to help a woman with a flat tire, and watches her get 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 heads for the University of Michigan to begin her internship but decides not to follow through. When Steve announces his intentions to stay in Chicago, Sam decides to leave town. 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.