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.
Craig introduces Dr. Peltrovich to the hospital; Chandler, Ehrlich and Morrison embark on a game of paint ball; Turner feels pressure from Auschlander when she has to do a risky operation on a litigious patient; Griffin tries to make amends with Wade and Rosenthal; Richard becomes self-conscious about his baldness.
Craig gets jealous when Peltrovich begins to steal his spotlight at the hospital; Fiscus treats a woman with leukemia who refuses treatment; Novino treats two teens who are reluctant to return to their home situations; Ehrlich has trouble getting anyone at the hospital to buy tickets to a banquet honoring him; an abused woman comes to the hospital intent on getting revenge on her husband.
Ehrlich's world is shaken by the arrival of his long lost parents; Kiem neglects her visiting husband to spend time with a patient who just lost his wife; Axelrod nearly loses a patient after deferring to Novino and Griffin on a diagnosis; Luther is reunited with Polly who wants to go off the medication that controls her Tourette's Syndrome.
Westphall finds out surprising news about Lizzie; Craig is able to track down John Doe at a book signing; prejudices surface when Chandler clashes with a veteran private practice doctor; Novino stumbles upon a black market organ trade being done in the mortuary; the board of trustees inform Auschlander of the hospital's uncertain future.
Ellen invites Griffin to stay at the Craig household; Novino is reluctant to put a blind homeless man back on the street after he no longer requires treatment; Wade has to be escorted around the hospital after losing her contact lens; Auschlander gets surprising news from an old flame.
Westphall and Auschlander must put together a plan to save the hospital; an obnoxious patient creates problems for the hospital staff; Axelrod's veterinarian father visits him at the hospital with his dog; Rosenthal's daughter returns from overseas looking unrecognizable; Turner must tell an expectant young couple that their baby may not be born healthy.
Josiah Bartlett from Boston General expresses interest in buying the hospital with an effort to recruit Craig; Morrison testifies at the parole hearing of the guy who raped him; Fiscus treats a former fraternity brother who is a dentist with fainting spells; Kiem is on edge when she cannot get a hold of her son; Ehrlich gets jealous when he sees Papandrao talking to Griffin.
Fiscus takes interest in an expectant woman who is believed to be artificially inseminated with his sperm. Three children get bored in their room and decide to wander around the hospital. Westphall is visited by a childhood friend who reminds him of an old pact. Craig and Auschlander look for ways to keep the hospital afloat.
Daniels is escorted from jail into the hospital for treatment and her homecoming does not turn out to be a happy one. Westphal reunites with an old friend. Chandler and Novino compete against one another to diagnose a patient. Rumors swirl about Ehrlich and Papandrao getting married in Mexico.