One month after St. Eligius was shut down, it is reopened by The Ecumena Corporation and its head of medicine Dr. John Gideon. Meanwhile, Dr. Craig is offered the opportunity to design an artificial heart, which the younger doctors jokingly call the ""Craig 5000.""
Gideon and Westphall argue over an AIDS clinic, Ehrlich looks for a mysterious woman on his wedding day, Kiem experiments with hypnosis, and Joanne blames Boomer for letting her kids go back to Seattle with her ex-husband.
The AIDS clinic becomes a showdown between Dr. Westphall and Dr. Gideon; Griffin tries to avoid his AIDS patient's homosexual lover; Fiscus' mother drops by for a visit; and Luther tries to help a man who insists he's pregnant and about to deliver.
The orderlies ask Auschlander to talk with Gideon about their grievances, Wade puts up with temporary lodgers, Rosenthal confronts an epileptic nursing student, and Craig gives Ehrlich marriage tips while they start work on a sheep's heart.
It's Halloween at the new and improved St. Eligius, and the craft-matic bed where Mrs. Hufnagel was crushed to death is apparently haunted. Meanwhile, Wade, Craig, and Ehrlich look for a heart transplant recipient and Chandler sucks up to Gideon in order to get promoted.
Dr. Craig and Ehrlich attend a meeting of the Cushing Society, an all male medical society; Wade gets herself into more surgery than she bargained for; Novino takes a special interest in two lonely children; Dr. Gideon offers Ellen a new career; and Chandler is made new chief resident.
Dr. Craig and Ehrlich attend a meeting of the Cushing Society, an all male medical society; Wade gets herself into more surgery than she bargained for; Novino takes a special interest in two lonely children; Dr. Gideon offers Ellen a new career; and Chandler is made new chief resident.
Craig proceeds with his artificial heart implant despite some questions about his choice of candidates; Morrison tries to deal with the departure of Joanne for Seattle and Dr. Craig becomes suspicious about the relationship between Ellen and Dr. Gideon. AIDS patient, Brett Johnston, and his lover are victims of gay bashing and as a result of his injuries, Brett is readmitted into the hospital.
Fiscus pulls one last prank on Gideon before turning thirty; Morrison and Novino compete to deliver the 100,000th baby at St. Eligius; Dr. Craig puts on the boxing gloves again; and Lucy walks the Freedom Trail with a dying man.
Axelrod's cousin Pee-Wee checks in and checks out Novino; Fiscus tries to help his father deal with his stroke; Mr. Spooner takes his first post surgery steps with the media in full attendance; and Dr. Auschlander considers his future medical treatment.
A man claiming to be the true inventor of the Craig 9000 kidnaps Ehrlich; AIDS patient Brett Johnston's rib injuries have led to pneumonia and he is now determined to break with his lover; Dr. Kiem helps Amy Jeffries, a lonely St. Eligius neighbor; Griffin treats a driven young broker determined to make a million before he dies; Lucy worries that she might be pregnant; Helen returns to work; the company that owns the hospital finds itself sued for infringement and Mrs. Spooner ends her husband's suffering.
Mr. Bevine returns for foreskin reconstruction; Dr. Auschlander seeks an alternative for a fellow cancer patient; Novino frets over Pee-Wee and tests Lucy, who has trouble telling Victor the news; Fiscus returns to work. but has trouble putting his father's death behind him; Morrison's false confidence as `Dr. Adam Logan' evaporates when Pete is rejected by an exclusive private school.
Judge Farnham checks into the hospital with an inoperable cancer (and asking for Floyd the Barber); Rosenthal takes Bobby Caldwell's death very hard; Dr. Craig searches for a date for a skating rink opening; Dr. Kiem is in the middle when she saves the life of a young black man shot by a Vietnamese gang member; Griffin befriends the new chaplain, who's a descendant of the hospital founder, Father McCabe; Novino and Luther compete on the ER simulator and Ehrlich tries to find his elusive parents.
Morrison counsels a family about genetic testing and Huntington's disease; Rosenthal's drug problem causes a death; artist Alex Corey does a shocking piece of performance art; the Craigs proceed with their divorce and the hospital undergoes a name change.
Phil returns from a training course at the Weigert home office; someone takes a shot at Dr. Gideon; Dr. Craig loses Flash during a rescue attempt by animal activists; the new security cameras upset Rosenthal, who continues to lose control; Novino tries to correct a misdiagnosis made 60 years ago, and a show is performed in the children's ward.
Fiscus can't understand his nihilistic cystic fibrosis patient or her punk friends; Dr. Gideon suspends Dr. Craig because of the Spooner malpractice suit; Ehrlich and Lucy are unable to console each other when she miscarries; and Rosenthal admits herself to the chemical dependency unit.
Dr. Craig, Ellen, Lizzie and Novino drive to Peterborough, New Hampshire to visit Dr. Westphall on his birthday; Ellen tries to deal with changes to her hometown; Novino stirs up a lady carpenter; Lizzie finally expresses her resentment; and Dr. Craig almost destroys his friendship with Dr. Westphall.
Wade and Kiley liberate their psyches during a study of OR infection vectors; Dr. Auschlander meets the son he never knew; Morrison and Novino grow closer as they work in the ICU; and Rosenthal adjusts to life in the chemical dependency unit.
Ehrlich stands up to Dr. Craig's verbal missiles; Griffin fails in an attempt to pass along spiritual support; Axelrod faces emergency heart surgery as a patient; Rosenthal finds it hard to face her children during family therapy; and Luther uses Penny's video equipment to record Dr. Gideon.
Brett Johnston's parents come to visit; even in death Axelrod doesn't get any respect; Rosenthal waits for her release while her roommate runs away; Luther proposes to Penny; and Dr. Craig returns to St. Eligius to do a multiple transplant.
An ebullient Novino pursues Morrison; Fiscus tries to revitalize his mother's life; Rosenthal returns to duty; Wade tries to help a dying child deal with her bitterly divided parents; Griffin tests positive for AIDS; Dr. Turner returns and helps Chandler come to a decision about his future; and the Oseranskys return to take Lucy to the ""Doctor of the Year"" dinner, which ends in a flaming disaster.
The Craigs' reconciliation faces its first test; Drs. Auschlander and Gideon struggle together to save St. Eligius when Weigert decides to get out; Novino pushes Morrison to decide between her and Joanne; Griffin places his future in God's hands; Ehrlich returns from his odyssey; and Fiscus' last E.R. patient is a lady from the opera...
But is it really over? The jaw-dropping climax culminates in a blue-collared dad placing his young autistic son Tommy Westphall's miniature St. Eligius snow globe on the living room TV set, having summoned him to dinner. ""St. Elsewhere's"" entire six-year saga had all been a figment of little Tommy's imagination!
