Ray helps an old friend escape from her abusive father. Dubenko volunteers in the ER but can't seem to handle a slow day. Abby and Kovac go baby shopping, while Neela gets unexpected and upsetting news from Gallant.
Dr. Nate Lennox, a former professor with ALS, is brought in as the progression of his disease is chronicled through his own flashbacks as he is treated by each of the doctors at one point. As Lennox wants to give up, Abby fights to convince him to keep on fighting.
An unexpected visitor puts Clemente in the middle of a domestic dispute. Meanwhile, Luka and Abby await test results on their unborn child; Neela struggles with her surgical elective and Pratt ends up with an unexpected suitor when he participates in a charity bachelor auction.
In Sudan, Carter and a colleague struggle to save a woman who was raped by a band of militants. Back in the ER, Clemente asks to return to work after the shooting incident, but Kovac refuses. Meanwhile, Neela and Pratt have a work dispute, and, in a related incident, K.J.'s father shows up again in the ER.
Weaver contemplates hip replacement surgery after she finds it hard to do her labor-intensive job. Meanwhile, Kovac tries to ease Abby's fears about raising a child together. Neela decides to attend a support group for military spouses but when she offers her opinions on the war, the meeting turns into a debate. And after Sam treats a fainting victim, she finds herself with an intriguing job offer.
Abby and Luka desperately try to keep a young woman brought into the ER with stab wounds to the neck alive. As her condition begins to worsen, Clemente steps in and tries a risky procedure on the girl in order to save her life. Meanwhile, Neela pulls an all-nighter in preparation for a speech at a surgeon's convention, Ray treats a man claiming to have swallowed a bottle of pills, and Sam decides to take a part-time job with Richard to help her with childcare expenses.
When two teens are in a car accident, Abby and Morris struggle to figure out what is wrong with the unconscious girl. Meanwhile, Neela gets a visit from her in-laws and discovers some troubling news. Kovac tells Abby that he plans to go to Africa and help Carter, but when he realizes Abby is not crazy about the idea, he decides to send someone else in his place. Sam starts her new job with Elliot and quickly starts to love the the perks.
Dr. Clemente's paranoia spirals out of control after he receives threatening mail from his girlfriend's husband. Abby senses something not right when a grandmother and granddaughter are brought into the ER. Sam's jailed ex-husband Steve is brought into the ER and everyone but Neela assumes he is faking sick. Meanwhile, tensions grow when Morris and Albright argue over a patient, Pratt heads to Africa to help Carter and quickly realizes how difficult life will be; Weaver finishes physical therapy.
Chaos reigns in the ER when two prisoners are brought in for treatment, but instead plot a violent escape. Their desperate actions place one doctor in harm's way, and forces one nurse to become a tool in their plan.
Weaver, Kovac, and the other doctors work frantically to try to save Jerry and a pregnant Abby, who were both critically injured during the shootout that left the ER in shambles. Meanwhile, Sam tries to escape from her ex-boyfriend and his criminal accomplices as they head north, but things quickly turn violent.
As Abby and Luka cope with their newborn's life and death struggle, the couple is shocked to receive a surprise visitor: Abby's mother Maggie. Meanwhile, Sam fears the prospect of criminal charges; Neela discovers that Tony Gates will be joining the ER team as an intern and Morris gets his job back while Weaver gets demoted.
Abby and Kovac discover both the joys and difficulties of raising a newborn; Morris is wrongfully accused of being a child molester; Pratt has his trial-by-fire when he has to handle the ER alone, juggling multiple traumas, teaching duties and a troublesome intern. Neela continues to be the target of her difficult supervisor, and Sam discovers her sons latest extra-curricular activity.
Curtis Ames, a carpenter who suffered a stroke under Kovac's care, sues him for malpractice. Kovac and Ames square off in court as each man's recollections of Ames' treatment are recounted via testimony and flashbacks. Meanwhile, Abby returns to work and must adjust to the dramatic changes in her life, and Pratt's early morning trip to the barbershop results in a new awareness of community need. Also, Abby and Pratt try an unconventional method for treating a heart patient and Neela tries a risky procedure which doesn't sit well with her chief.
Kovac anxiously awaits the verdict between himself and Curtis Ames but fears the worst. Meanwhile, Neela disobeys her chief's orders and also questions her feelings for Gates, and Weaver unwittingly steals the spotlight from Morris in his big television debut.
A belligerent young man who claims to have the flu turns out to be more than he seems, and presents a challenge to Morris and Sam when he refuses treatment. Abby's chance encounter with Curtis Ames leaves Kovac uneasy. Meanwhile, Pratt discovers a local church's risky drug exchange program, Neela and Gates square off, and Weaver gets an interesting offer.
A mysterious illness leaves little hope when a group of homeless kids enter the ER and one of them believes that Neela is a guardian angel in blue; Abby and Kovac clash over a possible case of domestic abuse; Pratt makes a shocking discovery about his brother, and Weaver is unexpectedly called into action when her television appearance becomes a real emergency.
Thanksgiving at County is quiet, with the normal number of routine (or nearly so) emergencies. But Abby makes up for the lack of excitement while returning to the hospital as the doctor on a helicopter transport.
Kovac and Gates treat a girl who appears to have been assaulted. When the police are no help with Ames, Kovac decides to confront the problem himself; Morris and other doctors work on a patient with an ice pick in his ear. Meanwhile, Ray tries to keep his new relationship a secret and Pratt can't fully deal when his half-brother officially comes out. Also, a new male nurse arrives.
It's Christmas in the ER. A homeless boy sends Gates and Ray on a mission. Meanwhile, in the ER, Neela oversees an unusual kidney transplant case; Sam takes a stand when a patient is dumped in an alley by another hospital; and Morris plays Santa for a special girl and learns the meaning of Christmas.