Weaver returns to the emergency room after a self-imposed sabbatical of three weeks, wondering how her newfound lesbian identity will affect her workplace relationships. Having purposely allowed a mass murderer to die, Greene must keep the secret amidst the scrutiny of his superiors.

Carter is overwhelmed by patients from a rock concert riot. Benton's former girlfriend is killed in a car accident. Newly promoted to chief resident, Chen panics and misdiagnoses a patient. Kovac angers Abby by flirting with a waitress.

Greene's daughter comes to live with him and Corday. Carter and Abby become more intimate. Chen must prove her skills while saving a baby. Weaver terminates Malucci after witnessing him having sex in an ambulance.

Dr. Susan Lewis arrives, looking for work in the Chicago area again. Greene hires her, over Weaver's objection. Chen nervously attends a risk management review, accompanied by the unforgiving Weaver, to discuss a patient who recently died under Chen's supervision.

Lewis faces a hectic first day back at County General. Benton and Roger become frantic when they can't locate Reese. Carter's grandmother is brought to the emergency room. Carter and Abby deal with inept medical students.

Corday's ordeal, caused by the recent infection-related deaths of several of her patients, worsens when she is closely observed by a stern taskmaster. Corday is outraged when a county investigator accuses her of deliberately euthanizing the patients, who all happened to be elderly.

A new medical student, Michael Gallant, arrives in the ER. He's supposed to be working under Dr. Carter's supervision but his grandmother is unwell. Elizabeth Corday is convinced that other doctors are refusing to work with as a result of the mysterious deaths.

When a torrential rainstorm pounds Chicago, patients deluge the emergency room while Weaver speeds to an accident site. There, she finds a pregnant woman, Vicki lying injured inside a wrecked ambulance while live power lines spark. Fourth-year student Michael Gallant makes a dangerous decision in order to help.

Peter Benton continues his court fight against Reese's stepfather, Roger, who seems to have the upper hand. When a woman is accidentally shot during a gas station robbery, Dr. Corday tries to convince the husband to let them harvest her organs. A 15 year old boxer is brought in with a head trauma after sparring with his older brother. Newlyweds are having trouble when she constantly breaks out in a rash; Carter thinks he knows the cause.

Benton commits perjury on the witness stand in order to gain custody of Reese. When Romano refuses to give him a more even schedule, Peter resigns and seeks a job at the clinic where Cleo is newly employed. Benton is granted custody of Reese and he and Cleo decide to move to the suburbs together. Meanwhile, Carter's father visits for Christmas with the news that he's getting divorced, Weaver and Sandy Lopez finally go on a date, and Abby catches Nicole in the maternity ward, recovering from an abortion.

Abby helps a distraught boy whose mother died of a stroke; a man with schizophrenia, who once stabbed Carter and killed a doctor checks into the ER.

An injured and condemned murderer wants to die in the ER rather than await execution; Abby advises a neighbor to seek shelter from her abusive husband.

An accidental overdose brings Drs. Green and Corday's baby into the ER.

Greene confronts Corday when she orders Rachel out of their home; Abby tries to protect a battered neighbor who refuses to press charges against her husband.

After Dr. Corday moves out, Dr. Green fights loneliness and pain by immersing himself into his work. He is treating a father in the ER who severely burned himself while experimenting with illegal drugs. Abby fumes when the man who beat her is released and moves back in next door; the returning Jerry clashes with fellow desk jockey Frank.

After some staff members are caught going through a dominatrix's bag, Weaver makes them attend a sexual harassment seminar, where they learn about each other.

Drs. Corday and Greene are awkward when working together in the ER. Dr. Weaver treats victims of an intense fire that may take the life of a dear friend.

As Dr. Greene's brain tumor begins affecting his coordination, he becomes concerned that his fate will be similar to the terminally ill patients he treats.

When Dr. Lewis gets a hysterical call from her niece, Susie, she hurries to New York to search for the child and her sister Chloe. The crossover continues on Third Watch S03E19 Unleashed

Dr. Carter reads a letter from terminally ill Dr. Green to the ER staff. Dr. Weaver lashes out at a mentally challenged patient. A terminal, homeless man continues asking for Dr. Green.

Dr. Greene's final days are spent in Hawaii with Rachel, teaching her to drive and surf. When he suffers a seizure, Elizabeth is called. Mark refuses to go home. He manages to make amends with his daughter before his eventual death.

Just when the ER is understaffed and swamped, two children who were brought in turn out to have full blown smallpox. The entire ER must be locked down. The staff needs to improvise while they battle not only the disease but also frayed tempers.