Abby, Carter, Chen, Pratt and homeless Stan will be confined to the ER for two weeks, while all of the other patients are evacuated and sent to different hospitals. While on the roof arguing with Luka about the use of a helicopter, Romano backs up into the tail rotor, and has his arm severed above the elbow. Anspaugh arrives to perform surgery, and reattaches the arm. Susan is stuck on the roof with a dying patient. After 2 weeks, the ER reopens. While all of this has been going on, Elizabeth has been in London, working at her father's hospital, where her supervisor doesn't like the American mannerisms and vocabulary she's picked up. She ultimately decides to return to Chicago.

Two months after the lock down, a new group of med students arrive in the ER to pandemonium, caused by the closure of another city ER. Corday returns to the ER, having lost some of her bedside manner. Gallant is on a psych rotation, annoying the ER staff. Romano continues physical therapy. Weaver is acting strange, she breaks down and cries in front of Elizabeth. Pratt brings a man, pronounced dead, back to life.

Lewis treats an end-stage Huntington's patient, whose mother has already watched her husband wither from the disease. Abby's brother Eric, an Air Force traffic controller, visits on his way to a new post in Nebraska. Carter tends to a 12-year-old drug-addicted prostitute with a serious STD, until her pimp shows up and whisks her away. Pratt aggravates a drug-seeking man who comes back brandishing a gun at Chen and Abby and demanding Demerol. Abby gives him his shot but purposefully ODs him. In the aftermath, Carter flips his lid, demanding better security and the installation of metal detectors. When Weaver refuses, Carter leads a walkout. Weaver eventually caves, albeit before telling Carter that he must fire three senior nurses by tomorrow to make up the budget. Abby, Lewis and Chen go to a concert to decompress.

Weaver makes a mistake on live television while demonstrating flu shots, inadvertently sticking two reporters with the same needle. In the bathroom later, Susan and Abby catch Weaver in a stall with a needle. Weaver confesses to Susan that she's taking hormones. Carter, assuming Susan knows already, tells her about Abby's drinking problem. Abby becomes nurse manager, and argues with Carter about her drinking. Luka flirts with a patient's mom and is caught emerging from a storage closet with her. Gallant has a rough day: Pratt butts in on a patient of his, and Stella Willis dies because Kayson didn't bother with thorough treatment.

On a busy Halloween night, Carter and Abby are the only staffers in costume when victims of an apartment building fire pack the ER. Corday takes on a new med student for a surgical rotation--Paul Nathan, who suffers from Parkinson's disease, and only decided to pursue medicine after his diagnosis. Despite a difficult first day, both professionally and medically, Nathan makes a difficult diagnosis. Romano's rehab lags behind his expectations, and he begins to doubt his role if surgery is no longer an option. In a moment of personal weakness, he tries to express his feelings for Corday. Weaver continues to display erratic behavior, raising staff suspicions she might be going through menopause. Luka's affair with Chuny is revealed, and tensions rise when he treats a patient with a perpetual erection.

Corday clashes with new surgical resident Paul Nathan regarding his intervention into the treatment of a sickly young woman, Alison, who has signed a "do not resuscitate" order. Abby wonders about the erratic behavior of her visiting brother Eric, and feels conflicted over a nurse's official complaint against Kovac. Meanwhile, Pratt comforts Chen after a patient threatens her, and Corday suspects that an unconscious, 14-year-old female patient has been sexually assaulted.

Abby fears the worst when her brother Eric suddenly disappears. Carter and Chen treat a frightened Chinese immigrant nanny, Tong-Yi, whom they suspect was impregnated by her employer. Meanwhile, new surgical resident Paul Nathan, who is struggling to overcome a physical disability, tries to help in the emergency room—but his fellow doctors do not appreciate his advice to patients. Kovac goes to extreme lengths to find an eye specialist to treat a young gunshot victim. Gallant and fellow medical student Erin Harkins engage in an escalating competition of medical knowledge. And Weaver gets some much-needed good news.

Abby's family nightmare continues as she and her mother Maggie search for Abby's missing brother Eric, who Abby suspects is suffering from serious mental problems. The two women go to a Midwestern air force base, hoping to prevent Eric from being court-martialed for being absent without leave. Carter struggles to get out of Chicago to join Abby. Meanwhile, Corday treats a family of patients who, while building a snowman, were severely injured after being struck by a truck driver. She must help the father, Stuart, make a life-or-death decision. Corday also sympathizes with troubled surgical resident Paul Nathan as he struggles with the increasing symptoms of his physical handicap.

Abby is distressed when her mother interferes with Eric's treatment at a psychiatric hospital. Pratt treats a frightened young girl who has been injured in an auto accident and desperately wants to hide a secret. An unhappy Luka forms an unlikely bond with a lonely elderly woman who makes him a surprising offer. Chen is overcome with upsetting memories when a baby is abandoned in the emergency room. Pratt takes action after Leon is fired from his menial job.

The past 24 hours play in reverse after Luka gets into a car accident with Erin. Luka was forced into working hungover after a staff Christmas party, leading to a patient being brain dead. At the party, he confesses to Abby that he misses her before an oblivious Carter interrupts.

When Pratt is witnessed bringing a gun into the emergency room, Carter feels compelled to defend him. However, Pratt's erratic behavior makes Carter reconsider. Meanwhile, Weaver hopes to keep her pregnancy a secret, but physical complications might compromise her plans. Lewis warily watches self-destructive patient Chip Mealy, who admits to molesting young boys. Romano warns guilt-stricken Kovac not to admit to a grieving mother that his miscalculation caused her son's death. Chen treats high school students who overdosed on Ritalin. And Gallant confronts the scheming young wife, Koko, of an aged, dying man.

Weaver confronts a dilemma when influential alderman John Bright, seeking treatment after a fall, tests positive for syphilis—potentially damaging information that could become public. A sympathetic Kovac defies conventional ethics when he tricks a seriously injured patient who refuses to leave his dying wife's side into believing that she has already expired. Pratt ignores a dying mother's wishes in hopes of keeping her kids out of foster care, while also dealing with more problems with Leon. Meanwhile, Carter's family fortunes fail to pay off for an ailing doctor running a local clinic. Weaver and Kovac differ on what to do with a young boy whose medical history suggests repeated child abuse.

Carter's plan to help an ailing doctor leads to a dead-end — and a decision about his own career path. Pratt intervenes after a burglary lands Leon's pal in the ER, along with the cop his so-called friends shot. Kovac goes AWOL from his job after Weaver is unsympathetic to his depressive spiral. Alderman Bright returns, bearing financial gifts of gratitude for Weaver. Corday is caught off guard by hot-shot new surgeon, Dr. Dorset, and Romano risks his standing at County by overseeing an operation he is incapable of completing. Abby's brother Eric, now on his bipolar meds, visits and reconciles with her.

After taking care of a wounded prostitute and bringing her case to the attention of social services, Chen tells Pratt about giving up her baby for adoption. Romano is furious after Anspaugh notifies him he's not allowed to take part in surgeries. Kerry gets a promotion, due to Alderman Bright's aid. Susan has a blind date. And while Carter is out of town, Abby receives word that Eric's private plane is missing.

With Eric still missing, Maggie returns to town. Carter tells Abby he wants to marry her. Weaver gives Luka an ultimatum regarding his job. Pratt digs himself into a deeper hole with Chen during his stint with the EMTs. Sean Simmons returns with pneumonia.

Three people are murdered at Doc Magoo's. One person is severely injured. In a search for the suspects, Gallant and Pratt are pulled over and arrested while returning from the gym. They take the arrest personally, and they later confront the officers when they are brought to the ER after being in an accident. Carter wants to pop the question on Abby, but decides it's not the right time. Kovac is forced by Weaver to see a psychiatrist. Lewis spends time with Sean, as his time winds down.

Alderman Bright returns to blackmail Weaver into treating his gay lover for syphilis (off the records, of course). Unfortunately, the man dies from an allergic reaction to penicillin and Kerry is forced to cover up her mistake. Carter and Abby come to terms with their ailing romance. Luka has a very unconventional therapy session. Romano's condition forces Anspaugh to replace him as chief of staff… with Weaver.

After being pushed out of his job as Chief of Staff by Kerry, Romano takes control of the ER and wreaks havoc and manages to get himself beaten up in a bar after work. Kovač implores Weaver and Corday to help him arrange a pro-bono operation for a dying Croatian child. A young woman with terminal cancer must make a choice between life-prolonging chemotherapy and the life of her unborn child. Pratt buys a birthday gift for Chen from a street vendor whose foot was run over by Elizabeth's nanny. Susan's husband (who she married the same week she met him) unexpectedly shows up from Las Vegas.

Abby treats a psychotic patient who has overdosed on his medication while Eric, Abby's brother, finally calls. Kovač welcomes an old friend - a fellow Croatian doctor - to observe the chaos of an American inner-city hospital. Gallant and Pratt receive their match letters. Carter receives bad news about his grandmother. Romano discusses grave options about his arm with Corday.

Kovac defies the rules to get a dying Croatian boy to Chicago in a race to save his life. Carter's sad family gathering is interrupted by Abby's mentally troubled brother Eric, who has left his voluntary care facility. Lewis and Chuck annul their marriage but choose to continue the relationship. Perez, a baseball player with a serious heart ailment, is treated on the eve of his pitching debut with the Chicago Cubs. Carter tries to prevent grieving gang member Curtis from seeking vengeance. A tormented Romano makes a dramatic decision about his mangled arm.

Carter's day shift and Pratt's night shift (his final shift at County) are intercut. Both men have extremely busy days. Doc Magoo's burns down. Luka calls Carter from the Congo and asks for help. Carter decides to go. Pratt decides to stay at County. In other parts of the hospital, Romano has his now-useless left arm amputated.

Carter travels to the Congo. During the course of his two weeks there, he learns how much different the conditions are against what he's used to. Luka decides to stay for a while as Carter heads back to Chicago, ending up at a sleeping Abby's bedside.