Dr. Carter, Abby and other staff of the ER are quarantined as the CDC investigate a mysterious, deadly outbreak.

After another hospital shuts down, the ER is flooded with patients. Dr. Pratt resuscitates a heart-attack victim who had been pronounced dead.

Dr. Carter leads a walk-out of staff protesting lack of security in the ER.

Carter is concerned when he learns that Abby is drinking socially when the girls from work get together. Abby, however, doesn't appreciate his concern. Dr. Weaver embarrasses herself on television. Michael Gallant is frustrated when the resident cardiac specialist, Dr. Kayson, dismisses his diagnosis of a patient who subsequently dies. Dr. Pratt decides to report an Army Ranger who tried to commit suicide even though Gallant had decided to give the soldier the benefit of the doubt. Dr. Corday has to deal with a severely injured woman who is more concerned about her Alzheimer's-afflicted husband. Dr. Kovac's sex-addiction extends to having sex in a supply room with a young patient's mother.

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 decided to pursue medicine after being diagnosed. 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 think his role in 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 about her menopause. Luka's burgeoning sex addiction worsens, as an 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, Abby's former lover. 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. He is actually AWOL and she forges Carter's name to obtain his medical records. 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 (Parkinson's disease), tries to help in the emergency room but his fellow doctors do not appreciate his advice to patients. Unable to quench his sexual appetite, Kovac also gets into trouble in his professional life, despite his admirable resolve 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 searches for her missing brother Eric, who she suspects is suffering from serious mental problems. Gallant accompanies her to his military base where they find Maggie, whom Eric turned to for help. When he's transferred, Abby and Maggie 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.

Harkins faces a tough call while treating a troubled teen involved in a car crash with her dad; Abby races to stop Maggie from taking manic-depressive Eric out of treatment; and Kovac hits a new low when an elderly woman tips him for his medical services. Meanwhile, an abandoned baby dredges up painful memories for Chen; and Pratt goes to bat for Leon after he's fired from his job for stealing.

Dr. Kovac's speeding causes a crash on an icy road. The ER staff treats angry elves and a female hockey player with a head injury.

Dr. Pratt brings a gun into the ER; Dr. Weaver tries to conceal her pregnancy; a woman plots against her dying husband; Dr. Chen treats math students who overdosed on an unknown stimulant.

Dr. Weaver is in a difficult situation when an alderman tests positive for syphilis. Dr. Carter is impressed when he meets a man who runs an inner city clinic.

Dr. Pratt's disabled roommate leads him to a wounded thief. Dr Carter decides to practice medicine in Chechnya. A doctor makes a pass at Dr. Corday.

Abby's troubled brother is missing. A car runs into a crowd of teen girls. The alderman with syphilis gives Dr. Weaver a promotion. Dr. Lewis looks forward to a blind date.

Abby comes close to breaking down trying to deal with her mother. Dr. Pratt goes for his required paramedic ride-along. Dr. Weaver confronts the man who stole her purse. Dr. Lewis has a teen admirer.

The police question Drs. Pratt and Gallant about a rampage at the diner across from the ER. Dr. Lewis befriends her teen admirer, a cancer patient.

Dr. Weaver bends the rules and treats the Alderman's lover for syphilis. Dr. Kovac's patient claims she was sexually abused at a boot camp for troubled youth. Dr. Carter treats a women with a nasty personality.

Dr. Romano seizes control of the ER and manages to offend everyone. Dr. Kovac asks Dr. Corday's help in the quest to bring a sickly Croatian boy to the U.S. for medical treatment.

A psychotic patient threatens Abby. Dr. Weaver suspects a woman poisoned her own baby. Dr. Romano continues to make rash judgments.

Dr. Carter tries to prevent a grieving gang member from going after vengeance. Dr. Kovac races against time to save a Croatian boy's life. A baseball player gets treatment for a heart problem.

It's Greg Pratt's last shift at County General and he treats a number of cases that were started by John Carter on the day shift. They treat a 12 year-old near drowning victim who has little chance of recovery; a Buddhist nun who has a special gift of seeing another's inner self; a woman who is convinced that the day's solar eclipse signals the end of the world; a drug addict who scams both of them for pain medication; and a pregnant woman who had her baby torn out of her womb. Dr. Romano has his re-attached arm amputated. Carter receives a call from Luka Kovac asking if he can come to the Congo and help out. Abby is none too pleased. Meanwhile, Doc Magoo's burns to the ground.

John Carter arrives in the Congo to find that Luka Kovac is away at a distant clinic administering vaccinations to the local population. He also finds appalling medical conditions. Too few nurses and doctors, limited equipment and few medical supplies are par for the course. That aside, he gets s great deal of satisfaction from the work he does. He meets Gillian, a Canadian nurse, and learns that she and Luka have become close. He tries desperately to save the life of a severely wounded man which pays later dividends when their camp is invaded by rebel troops and their lives are threatened.