Dr. Chandler decides to do his volunteer work at the Boston Women's Clinic where protesters caused criminal damage and were impeding the operation of the clinic. The young mentally challenged girl, Pru, is scheduled for an abortion at St. Eligius; Dr. Morrison is unwilling to perform his job as her attending physician because of his personal beliefs. Luckily, Dr. Erlich is set to perform the abortion. A bomb explodes at Boston Women's Clinic; no one knows if Dr. Chandler survived. When their patients are brought to St. Eligius, Dr. Auschlander receives a telephone ...
A bomb is planted near the hospital's gift shop; Fiscus is unhappy when he is forced to do his community service with the elderly; Rosenthal must deal with Papandrao both at work and in the courtroom; John Doe is close to discovering his true identity; Ehrlich and Chandler differ over how to treat a couple that is struggling to conceive.
The matriarch of the wealthy political Endicott family comes to the hospital for an extended stay; Auschlander is less than thrilled about the Endicotts being at the hospital; Morrison must undergo surgery for the first time; the Valeres finally make a decision on the future of their family; after making an embarrassing mistake on one of his patients, Axelrod is asked to treat a gorilla; Fiscus has second thoughts about his engagement to Mona.
The Endicotts deal with the aftermath of traumatic events. Caldwell struggles to come to grips with his prognosis. Ehrlich meets a teen with growth problems while doing his community service. Fiscus is leery about taking his relationship with Clancy to the next level.
St. Eligius' 50th anniversary spurs memories, including its opening in 1935 under the leadership of Father Joseph McCabe, the arrival of recently emigrated Helen Rosenthal and Mark's return as chief of surgery, Mark's bypass on Patrick O'Casey and the death of Maureen Westphall. Morrison struggles to diagnose a difficult patient and cope with the loss of Pete to a kidnapper.
Morrison still tries to find out what is wrong with Terence O'Casey and is frantic as to where his son is. In 1935, Westphall's entire family, with the exception of his father, is killed in an accident. In 1945, Westphall was so unruly that Father McCabe resorts to an unusual tactic to straighten him out. Auschlander arrives and has to deal with anti-Semitism and meets the woman whom he would later marry. O'Casey's parents come to visit their three-year-old daughter, who is sick. In 1955, Craig, an intern who acts like Ehrlich, was learning under the eye of Dr. ...
Axelrod and Fiscus are sent to a medical conference in California; Ehrlich treats a football player will do anything to get another chance to play; Morrison must tell a child that one of his legs will need to be amputated; the Craigs seek counseling; Novino's first day on the job as a doctor does not go very well for her.
Alex Corey is brought back to the hospital to paint a portrait; Chandler does his community service at a crisis hot line and gets a suicidal caller; the Craigs' marriage continues to show strain; Axelrod struggles for self respect; Westphall invites Novino over for dinner.
Novino treats a cartoonist with a life-threatening condition; Westphall asks Rosenthal for advice on his feelings for Novino; Morrison performs his community service at a prison; Ehrlich must treat Mrs. Craig and is very leery about diagnosing her with anything for fear that it will jeopardize his working relationship with Dr. Craig.
Turner returns from Mississippi; Chandler is nervous about the status of his relationship with Turner; Auschlander ends up being in the wrong place at the wrong time when he ventures to a property that is owned by the hospital; Craig becomes more irritable after temporarily giving up custody of his granddaughter.
Westphall and Auschlander don't see eye to eye on plans for an adjoining property; Turner gets attached to an orphaned baby; Luther fears that he might never be more than an orderly; Rosenthal is visited by her reformed son and first husband; Novino gets plenty of male attention at the hospital; Ehrlich joins Chandler at a protest rally; the Craigs argue about their granddaughter's baptism.
A mentally-disturbed man who thinks that he is the city of Boston roams around the ER. Novino accompanies Westphall to the Doctor of the Year banquet. Craig has an auto breakdown which causes him to miss the awards ceremony. Ehrlich is torn when he gets an offer from Boston General. Axelrod tries being less amenable to other people; the third year residency list is released.
The hospital's founder, Father McCabe, 90 years old and stricken with ALS, comes to visit the hospital; Craig gets some bad news regarding his hand injury; Morrison returns and gets a surprise in the morgue.
Craig tries his first surgery since his hand injury; Wade is depressed after splitting with her husband; Griffin, the new resident, clashes with Rosenthal; Fiscus and Axelrod get X-rays for a patient they believe is tennis player John McEnroe; Morrison introduces his new blended family to everyone.
Craig has trouble accepting the fact that the hospital hired a new Director of Surgery; an elderly woman from an adjoining apartment spies on the goings-on at the hospital; Fiscus stands up for a sick elderly man whose daughters are intent on putting him in a nursing home; Lucy invites Ehrlich to a family dinner.
Craig has trouble adjusting to life outside of the hospital; Axelrod abruptly walks out while examining a patient with a colostomy bag; Luther faces opposition in his training as physician's assistant; Fiscus and Auschlander go to the home of a dying patient who is being cared for by his estranged daughter.
Westphall has difficulty dealing with the parents of a terminally ill teen who pretend that nothing is wrong; Craig decides to write his memoirs but has trouble focusing; Griffin plays Birch and Novino against each other; Turner gets in the middle of a difference of opinion between Morrison and Chandler regarding a diagnosis.
Craig gets John Doe to help him type up his memoirs; Turner faces a moral crisis when one of her patients refuses to accept blood due to her religious beliefs; Griffin sells out Novino and Birch in order to save himself; Ehrlich and Papandrao try to sort out their relationship after the news of their sexual encounter becomes public.
John Doe takes on his next persona: Dr. Craig; Griffin seduces Lizzy, not knowing that she is Westphall's daughter; Luther decides to give his Physician's Assistant training another shot by helping to diagnose a patient with involuntary tics; Wade and Chandler treat a patient who unsuccessfully tries to climb the hospital ledge.
Craig initiates a search for John Doe who left the hospital with his manuscript; Axelrod is put in charge of a 14 year old medical student; Morrison continues to suffer emotional damage stemming from the prison rape; Auschlander is met with resistance when he tries to implement a drug testing program.
Westphall begins to doubt the long term viability of his relationship with Novino; Fiscus' estranged father comes to visit him in the hospital; Kiem begins to sees the writing on the wall when Craig returns; Auschlander finds that he has things in common with a rabbi who is a patient at the hospital.
Westphall befriends a well-respected Irish author who turns out to be a raging alcoholic; Craig attends the hearing to allow his housekeeper's husband into the country; Ehrlich takes an interest in Papandrao's new boyfriend; Rosenthal confronts McPhail about her suspicious behavior; Axelrod has a string of bad luck.