Fiscus gives the new residents a tour of the hospital. A nun must decide whether to disconnect life support when her fellow sister, injured in a car accident, is declared brain dead. After stalled negotiations with management, the nurse's union considers striking. Three city firefighters are rushed to the hospital after suffering serious burns. Clancy tells Jack that she is pregnant but has no plans on keeping the baby.
Sister Domenica threatens to take the hospital to court over the right to disconnect Sister Teresa's life support. Caldwell continues to treat the injured fire fighters. Fiscus treats a child whose only relative is a woman claiming to be his fairy godmother. Ehrlich teaches a sex education class to bypass patients. Westphall is forced to reinstate Peter White. Clancy decides to go to an abortion clinic without Morrison's support.
The hospital continues to be hurt by the nurse's strike for which a deadline is set. Papandrao is forced to leave the picket line to help Ehrlich during an emergency operation. Martin is raped for the second time. Craig hires Luther and Warren, both unemployed due to the strike, to fix a hole in his wall.
Auschlander feels negligent when a long-term maintenance worker develops asbestosis. White desperately attempts to locate his children. A mental health patient admits to the hospital rapes. One of the firefighters develops complications in his treatment. Ehrlich's bid to meet the new nutritionist turns into a disaster.
Auschlander hires Joan Halloran as his assistant. White has a reunion with his wife and kids. A gun is stolen from the ER. Axelrod thinks there is something wrong with him. Rosenthal begins an extra-marital affair. One of the firefighters being treated is happy with the results of his plastic surgery while another cannot wait to leave the hospital.
White is shot and rushed into emergency surgery. Morrison tries to find a psychological cause for a boy's asthma. Ehrlich incurs the wrath of Craig after agreeing to appear on a television news show. Worn down by stress, Auschlander considers retirement.
The last of the firemen is discharged and surrounded by family, he drives away on his squad's engine, horns blazing and Caldwell standing on the sidewalk smiling and wearing his firemen's hat. Morrison' neighbor was babysitting Pete when he had to rush his daughter to ER; in the ensuing fight to save her, Morrison gives her father options where he can be more than a spectator. Two very cantankerous brothers check in and cause many more problems than the staff anticipates. Kathy is given a document requiring trust, tact and understanding. Cavanero gets in over her head...
Auschlander's friend, a world-renown doctor who migrated to Africa 40 years ago, comes to visit the hospital. Ehrlich is advised to make his TV spots more entertaining. Craig must remove a potentially exploding bullet from a shooting victim. Rosenthal, with her 45th birthday approaching and husband walking out, has a midlife crisis.
Wyler finds himself out of his depth when he observes Tshalla's kidney transplant. A Caribbean medical school with questionable credentials that tries to recruit Luther turns out to have a "graduate" working at St. Eligius.
With the First Lady coming to Boston, St Eligius is chosen by the Secret Service to care for her, if needed. As the staff prepare and enter alert mode, Ehrlich reports a case of potential child abuse and Shirley Daniels returns.
Chandler must try convince a clown with MS to quit the circus; Axelrod meets with a lawyer about Mrs. Hufnagel's estate; Morrison hits a low point in both his professional and personal life; Caldwell's facial surgery patient expresses her feelings for him.
Luther is rushed into surgery after losing his hearing in a boiler room explosion; Auschlander gets some very sad news while reading the paper; Axelrod puts Mrs. Hufnagel to rest; Craig gets some surprising news about his son.
Westphall, Craig and Auschlander go to the bar "where everybody knows your name," manned by a skeleton staff (Carla plus patrons Norm and Cliff). During the meeting at Cheers, Westphall announces he is quitting medicine. Craig later meets an old mentor who is suffering from advanced dementia and doesn't recognize him.