Phillip is unable to save a promising young boxer who succumbs to the fatal effects of steroids his father gave him to enhance his performance in the ring; a pregnant young teenager carrying a baby with a heart defect seeks Alan's help when she is unable to find adoptive parents for her infant; Aaron fires Angela after his tax audit reveals that she's been embezzling money from his pension plan.

When the gun belonging to a critically wounded police officer drops out of his holster in the E.R., the distraught brother of a man waiting for a donor heart picks up the weapon and threatens the staff unless his brother receives an immediate transplant; as Aaron and Danny operate on the wounded officer, one of the exploding bullets with which he was shot goes off and severs two of Danny's fingers; Geri performs a successful reattachment, but Danny may be facing the end of his career as a surgeon.

Dr. Kronk's feelings towards his girlfriend undergo changes when he find out about her past. Geiger's heart patient develops an aneurysm which would take him off the heart recipient list unless highly experimental methods are tried. Meanwhile, Dr. Hancock's ejection from his clinic leads to bringing the HMO provider into the courtroom.

When the Board of Health closes the hospital doors after several patients die from a deadly staph infection, the staff scrambles to find the source of the infection; Jeffrey and Geri help each other work through feelings of grief, loss, and guilt.

Diane helps her friend Allison harvest sperm from Allison's comatose husband before his life support is turned off; Aaron realizes that the reconciliation with Camille isn't working, and they agree to go through with their divorce; Billy takes Danny to task over his medical mistreatment of a mentally unstable woman; Jeffrey and Kate manage to put aside their differences over her cost cutting proposal for the hospital long enough to save the life of a young pre-med student; Alicia is christened.

Dennis struggles over whether he should listen to his gut, or to Jeffrey's advice, in treating a man who doesn't speak English; Aaron is upset when Alan gives Camille advice about their property settlement; after Billy recommends amputation to a man with a gangrenous leg, Diane offers the use of maggots as an alternative treatment, but the patient has a great deal of difficulty in overcoming the ""ick"" factor of Diane's suggestion; Phillip seriously injures his opponent in a charity boxing match; Aaron and Camille sign the papers that finalize their divorce.

A violent storm on Halloween night knocks out the hospital's power immediately following the arrival of several auto-accident victims. Nyland and Atkisson briefly renew their romance. A new doctor shows up for duty, and is immediately put to work delivering a baby.

Judge Aldrich's tenure as Alan's replacement is cut short by illness; Amy, an old friend of Danny's from medical school, joins the nursing staff and clashes with Camille over the care of a terminally ill patient; Kate and Billy hook up, but decide that they won't repeat the experience after they clash professionally during experimental laser surgery on an elderly cardiac patient; Amy rebuffs Danny's advances.

A heart-transplant patient returns to the hospital with chest pains and emotional and personality changes that challenge the notion of what really is exchanged in a transplant. Shutt is approached by a direct, self-confident psychiatrist who insists he perform psychosurgery on a 12-year-old boy with an obsessive-compulsive disorder that severely limits the life he can lead.

A friend of Kronk's seeks his advice about a health problem she thinks resulted from her sex-change operation. Austin treats an impressionable teenage boy with a heart condition and a crush on her. Dr. Konstadt, off her medication, acts injudiciously when Shutt seeks permission from a reluctant board to perform surgery on Eric.

Tommy places a bid to buy out the hospital with the intention of firing Kate as soon as the deal goes through; as Valerie continues her affair with Danny, Jack lets Danny know that he's aware of their relationship; Elizabeth is readmitted after Andy beats her again, and Andy takes his revenge when Dennis attempts to help his sister escape the cycle of spousal abuse; a mysterious biohazard accompanies a patient admitted to the E.R., and immediately begins to fell the staff; after Kate pleads the hospital's case, Jack agrees to counter Tommy's offer, but only if Phillip fires Danny; Kate and Tommy threaten to expose each other's secrets; after Diane's work for the last two years is called into question and her grant money is suspended, she decides to go to Africa to do research with a colleague; Tommy courts Aaron's support; feeling under-appreciated and ill-respected, Camille resigns; realizing that Tommy will stop at nothing to destroy her, a desperate Kate flees with their daughter an

Kate returns to Chicago to face possible arrest and her ex-husband, as well as suspension at work. Aaron ponders Philip's bitterness over Aaron's apparent support of Tommy Wilmette. Dennis struggles to regain his health. Dr. Nyland returns to find a new doctor in charge of the trauma service. Kronk and Grad continue to quarrel as he prepares to leave Africa.

Kate cares for her dying father and gets some words of wisdom from Tommy when he brings Sara for a visit; Philip recruits Dr. Jack McNeil to head up orthopedics; Diane returns, only to find that Billy has remained in Africa and that her lab has turned into a storage room; Keith places himself in legal jeopardy when he decides to help an injured drug courier evade arrest; Aaron persuades Tommy to give the hospital six months to turn itself around with Philip at the helm.

Dennis and Jack clash over the best mode of treating the arthritic knee of a world class cyclist; Aaron makes a new friend when he takes on a new research assistant; Kate and Danny have their suspensions reviewed by the board; Phillip plunges back into patient care by performing an experimental procedure on a woman who exhibits unusual complications from a liver tumor; Caroline discovers that orthopedics are not for her; Dennis faces an emotional struggle in the aftermath of his shooting.

White supremacists on the run following a failed assassanation attempt against the President hole up in a grocery store with an injured member and demand a doctor from Chicago Hope to treat him.

After a gang member dies in the ER, the boy's mother claims that one of the doctors suggested they ""Let him die"" so a prosecutor calls in Wilkes, Nyland, McNeil and Watters for widely varying statements about what actually happened during the crucial time period.

Jeffrey Geiger drops by Chicago Hope to announce that he has bought a controlling interest in the hospital, and to perform a deicate heart operation on one of Kate's patients. Kronk is forced to take over caring for his father, who's afflicted with Alzheimers. Aaron and Jack ponder the meaning of religion and God when several people claim to be seeing an image of the Virgin Mary in the hospital lobby. Wilkes takes action concerning his future.

Gang warfare breaks out in the E.R.; Kate refuses to perform a heart transplant; Billy and Diane get back together.

The hospital prepares for the Doctor of the Year party, and several old friends drop by. Watters goes into a virus-induced coma and gets some words of wisdom from Alan Birch. Camille Shutt returns for the party and Aaron discovers he still has feeling for her. Dr. Nyland returns to the hospital and reveals that he has really changed his life. Geiger also visits the hospital.