Season Premiere: A frantic Sam and too-calm Luka report diabetic Alex missing after he runs away to find his father. Acting on information from the police, they follow a lead to Iowa, then eventually head for Colorado. As they travel, they discuss their relationship, slowly realizing they have very little in common. With Alex safe, Sam tells him the truth about his father and takes him to see him. In the ER, Susan, Pratt, and the nurses evaluate Ray, Neela, and Abby's first days as R2s, while each of them struggles to manage patients, new interns, and their first attempts at teaching.
A baby's life is endangered when the surrogate mother refuses a C-section. The biological parents, Ray, and Dr. Coburn disagree over the surrogate mother's treatment. Abby makes a difficult diagnosis on a young boy with a rare illness. Pratt is reunited with his father and his family. Sam tells Luka she's moving out, and Luka discusses the move with Alex.
For Luka, its the ultimate bad day, while new nurse manager Eve Peyton causes a stir in the ER. Luka and Kerry treat a severely burned, nameless man. Lukas treatment priorities for a woman in a skating accident and a boy with a head trauma result in a confrontation with Eve and a fight with the boys father. Abby helps a woman with the possibility of breast cancer make a difficult decision, then makes a discovery about Dubenko. Eve changes Sams schedule when she is unable to work with Luka. At days end, Abby provides a little TLC for an unhappy Luka, who wonders if anyone sees him for who he is.
Luka treats a woman who awakens after a six-year coma. Kerry returns to the ER, and clashes with Luka over the treatment of a baby injured in a car crash, while Neela treats the mother, who may have caused the accident deliberately. Abby learns about Dr. Dubenko's condition, and we learn his first name. Eve continues to challenge the nursing staff. Jerry gets struck by lightning.
There's a new attending in the house, Dr. Victor Clemente, and he has not made a great first impression. Clemente puts the residents through their paces, alienating Pratt and infuriating the R2s. Luka spends the day with recently awakened coma patient Blaire. As Luka struggles with whether or not to tell her about her accident, Blaire tries to make sense of her flashes of memories, resulting in a tragic event. In the ER, Luka and Clemente clash over her treatment, and Luka finally tells her what happened, possibly too late. Abby visits her cancer patient, leading her to get a baseline mammogram. Dr. Dubenko's surgery goes well, and Ray meets a new girl at a rock concert.
Theres monkey business in the ER as Clemente, Abby and Neela treat an infant chimpanzee. Pratt has a painful failed attempt at reconciliation with his father. Eve promotes Sam, then forces her to be involved as she fires Haleh. Ray discovers Zoe has chlamydia, and is underage. A recovering Dubenko trails the staff via a two-way television hook-up. A boy and his father are injured in a construction accident.
A kidnapped girl is used as a human shield by her kidnapper, and both are wounded during a shoot-out with police. While Abby treats the girl, she is caught in the middle of a dispute between Clemente and Luka over the girl's care. Neela assists Luka, then Dubenko, with the kidnapper. Later, Luka and Clemente argue over style and practice, leading Luka to put his name in as a candidate for Chief of Emergency Medicine. Abby takes her anger, and need for comfort, to Luka, who responds by kissing her. Gallants leave is delayed, to Neelas dismay, and Ray gets his comeuppance from Zoes father.
For Neela, what begins as a routine ride-along with Gates and Zadro turns into a defining day when a commercial jet and a private plane crash over Chicago. As Clemente manages the trauma in the ER, Pratt joins Neela on-scene. Luka and Abby wake up together at Luka's, but the crash soon takes them back to work, where the tension between Luka and Clemente continues. As patients flood in, Sam recalls Haleh when extra nurses are needed, and earns Eve's approval. Luka and Abby care for a patient with severe facial injuries while Pratt struggles to save a patient with a heart injury. Ray's youthful friend returns and creates a nuisance. As the day ends, Luka and Abby talk, and awkwardly decide to stay "just friends," while Neela has a welcome, and overdue, visitor.
Neela and Gallant make the impetuous decision to get married the same day. Kerry steps in to the Kovac/Clemente battle, encouraging them to get along, which results in a competition to be agreeable. Soon, Abby has her fill of them both, and teaches them a lesson when her patient crashes in CT. Morris, Ray and a somewhat rusty Kerry treat a man with hypothermia, leading Morris to take a stand regarding the best course of action. Luka, Clemente and Sam treat a boy with HIV whose mother refuses to believe HIV causes AIDS. At the days end, Neela and Gallant are married, despite Neelas doubts. At the reception, Luka and Abby celebrate his appointment as Chief of Emergency Medicine, then later decide maybe just friends isnt such a great idea after all.
Its Christmas Eve in the ER, and theres a new Chief of Emergency Medicine: Dr. Luka Santa Kovac, dispensing gifts and time off for honeymoon-bound Neela. Luka and Abby make plans for Christmas Day, but something is on Abbys mind. Kerry, Pratt and Abby treat a girl who is the victim of a random bullet fired by gang members, leading to a vigil outside the ER and a scared straight lesson, administered by Pratt, in the consequences of gun violence. Luka and Ray treat a woman with cancer who chooses quality time with her family over fighting the disease. Clementes former flame arrives, and the fires reignite, despite his efforts to resist. When a testy Santa insults a group of blind children, Eves extreme response forces Luka to bring in the nursing supervisor, and Eve is fired. Haleh auditions singers for the Christmas party and finds a surprising partner in Morris. Sam discovers the impact Steves imprisonment has had on Alex, and takes him to visit his father. At the end of the day, the gang gathers for the annual Christmas party. Luka and Abby exchange gifts, and Abby shares some big news with Luka: shes pregnant!
Two weeks after Christmas, Luka and Abby struggle with a decision about whether to keep the baby, which Luka wants but Abby is unsure she is ready to have. Abby treats three patients, each of whom triggers a flashback in which they discuss her fears, and what each of them wants. Luka discovers Neela has consulted with Dr. Coburn about Amanda, a pregnant, and very religious, 15-year-old girl, without first presenting to him. When Amandas parents refuse an abortion, the two differ over her care and whether Luka is influenced by his Catholicism. Later, Abby discusses her pregnancy with Coburn, and makes an appointment to see her. Luka removes Neela from Amandas case, before suggesting a termination option that Amanda can accept. Kerry takes a fall on the ice, injuring her hip, which may have to be replaced. Ray begs Kerry for time off to join his band in LA for a gig, but the band decides to move on without him. Clemente gets a visit from the two detectives looking for the missing Jodie, and later pays a quick visit to the drug lock-up for a little help. After her appointment, Luka finds Abby near the lake. He tells her they can still be together despite her choice, and she tells him she wants them to have the baby.
With Luka eager to get home, Clemente AWOL and Kerry temporarily off her feet, Dubenko volunteers to cover the ER briefly, but quickly becomes involved with a septic patient and her husband, who is unwilling to accept she will not improve. He soon finds himself at odds with both the ER and ICU staff over an appropriate course of treatment. Abbys excitement over her pregnancy means no sleep for Luka, and they head out for a bit of early shopping, and some dressing-room fun. Neela gets surgery as an elective, but is shocked to learn that rather that finishing his training in the US, Michael plans to return to Iraq. Ray helps Zoe escape to live with her sister when she arrives in the ER after a beating by her father, and Pratt fakes a blood test to help Darnell avoid arrest.
Emmy-winner James Woods guest stars as a Dr. Nate Lennox, a former professor of biochemistry with ALS who was Abbys early medical school mentor. As we follow the progression of his disease in reverse via a series of flashbacks, a different ER doctor treats him at each stage beginning with Neela as he must face the need for oxygen full time moving backward to Luka in the early stages. In the present, Lennox, now able to move only his eyes, and equipped with advance communication technology, is admitted with pneumonia. As Ray, Sam and Luka begin limited treatment under the proxy of his attendant, Abby believes Nate has communicated his own wishes, leading to a struggle to determine what course of action should be taken, and how long to fight the inevitable.
An unexpected visitor puts Clemente in the middle of a domestic dispute, and things dont look good. As the police sort out events, Luka, Abby and Sam try to save the victim in the aftermath of a shooting. Luka and Abby await important news about the baby. Pratt finds himself the center of unexpected attention at a fundraising event.
ER revisits Dr. John Carter and reveals what he's been doing since his departure from County. Now in Darfur, Carter and colleague Dr. Dakarai work alongside relief workers to treat famine victims. Back in Chicago, Luka and Kerry differ over Clemente's next step, and Pratt and Neela treat a hit-and-run victim.
Armand Assante guest stars as a patient who makes Sam an offer she might not be able to refuse. Luka must calm Abby's baby-related fears after an incident at the hospital places everyone at risk. Kerry makes a difficult choice, and Neela joins a support group.
Oscar-nominated Iranian actress Shohreh Aghdashloo guests stars as a Turkish mother whose daughter is brought to the ER close to death following a knife attack. Luka and Abby must struggle both to keep her alive and to understand the reasons behind the attack. But when surgery is delayed, will Luka put his trust in a risky procedure that might save her life? Sam makes a life-altering decision, while Neelas first conference presentation doesnt go exactly as planned. Morris' children come to the ER to visit him.
When Luka answers a call for help, he discovers not everyone is pleased. Will he honor his commitment, or ask a colleague to step in for him? Abby and Morris wrestle with the strange case of a car crash victim. Having made a change in her life, Sam finds herself enjoying a few new perks. Neela has unexpected visitors, with even more unexpected news.
Pratt departs for Africa with attitude to spare but makes his first contact with harsh reality before the plane lands. Abby senses something is not what is seems when she treats a 12-year-old and her grandmother (guest star Diane Ladd), then differs with Luka over the best course of action. A prisoner is brought to the ER with what everyone thinks is a fake case of appendicitis. Morris is dressed, and ready, to impress, but Albrights not. Its time for Kerry to return to work and Clemente doesnt know when its time to leave.
Pratt gets to work in Darfur, but soon finds his eyes opened to the need all around him. Debbie attempts to persuade Dakarai to seek treatment for his illness. Carter, Pratt and Dakarai find themselves in the middle of the conflict when a man and his pregnant wife arrive at the camp needing treatment, with trouble not far behind. Events force Pratt and Dakarai to make a dangerous journey.
Clementes behavior grows more and more erratic, forcing Luka to take a stand. Pratt returns from Africa, and works with Luka, Abby, and Sam on the case of a father and two sons who appear to have been beaten by gang members, but soon, Pratt learns the real story. Morris and Albright throw off some sparks. Dubenko has good news for Neela, but will two visitors bring something different?
Season Finale: In the aftermath of the tragedy befalling the ER, it's a seemingly ordinary day with the usual collection of patients. But soon, the day becomes anything but ordinary as two prisoners intent on escape come to the ER for treatment, along with a hidden conspirator. Their desperate actions place one doctor in harm's way, and forces one nurse to become a tool in their plan. Soon, gunshots ring out, another doctor hits the floor, and a staff member's life is in jeopardy. The medical staff rush to the aid of the injured and quickly discover one of their own is missing!