Shaun’s proposed treatment for a homeless patient puts him and Jared in Andrews’ crosshairs. Claire tries to overcome Melendez’s reluctance to do a risky heart operation. Glassman faces a difficult decision about his health.

As Shaun pushes back against Melendez in order to treat a gravely ill hospital janitor, Lim risks a lawsuit to repair a teenage girl’s ritual circumcision. Glassman exercises demanding oversight in choosing a doctor for his brain surgery.

While confronting Andrews about the residents’ grueling schedule, Claire joins Melendez to treat a patient for infertility. Shaun vows to stick by Glassman as he recovers from brain surgery.

Shaun recalls his own past to help an intellectually disabled teenager face separation from his mother, while Claire is put between an injured teenage rock climber and her worried parents. Meanwhile, Glassman's post-op hallucinations force him to confront a personal tragedy.

A patient asks Shaun and Park to keep an earlier weight loss surgery a secret from his husband. Claire and Melendez disagree over how to treat an anorexic woman who needs heart surgery.

Shaun and Morgan disagree over the seriousness of a concert violinist’s infected finger. Claire befriends a teenage patient whose parents believe she’s suffering from the stress of their divorce.

Claire’s effort to ease a dying college classmate’s pain is complicated by a surprising request. Shaun and Morgan negotiate the terms of an organ transplant between two headstrong brothers.

Dr. Shaun Murphy, Dr. Audrey Lim and Dr. Claire Brown’s E.R. patient is forced to reveal a secret to her husband after their treatment caused a complication. Meanwhile, Dr. Neil Melendez, Dr. Morgan Reznick and Dr. Alex Park struggle with a patient whose parents don’t believe in vaccinations.

Dr. Neil Melendez, Dr. Morgan Reznick and Dr. Claire Brown grapple with a patient’s wish to perform an operation that would keep him from acting on his pedophilic urges; and Dr. Shaun Murphy learns a lesson in empathy.

Dr. Shaun Murphy and Dr. Alex Park treat two patients who collapse at the local airport and whose symptoms point to an infection that may become airborne. The staff races to contain the infection before it spreads to the rest of the patients in the ER, resulting in a hospital quarantine during the holidays.

In the midseason return, the hospital is still in quarantine as Dr. Shaun Murphy continues to be overwhelmed by the chaos and noise in the emergency room; Dr. Morgan Reznick struggles to keep her patients alive, and Dr. Audrey Lim fights for her life. Meanwhile, Dr. Neil Melendez and Dr. Claire Browne must find a way to complete their patient’s bone marrow transplant, despite the quarantine.

In the aftermath of the quarantine, the staff of San Jose St. Bonaventure Hospital tries to return to their normal routines as the Department of Public Health office decides they need to review what transpired to restore public confidence. Meanwhile, as Dr. Audrey Lim recovers from the virus, she and Dr. Neil Melendez navigate their new personal and working relationship, while Dr. Shaun Murphy ...

While treating a surgical patient with ASD, Shaun and Morgan become intrigued by her “relationship” with her roommate. Melendez, Claire and Park work to save a woman with a mechanical heart, requiring equal parts engineering and medical expertise.

Dr. Andrews tries to convince a grieving family to donate their teenage daughter's face to another young girl whose face was horribly disfigured in an accident.

Shaun’s blunt honesty with a distraught mother of a critically ill newborn baby causes the new chief of Surgery to question keeping him on as a resident.

The new chief of surgery, Dr. Jackson Han, believes Dr. Shaun Murphy is a liability more than an asset and works to keep him out of the operating room permanently.

Dr. Shaun Murphy is desperate to join the team on a dangerous procedure involving a patient’s tumor removal. However, having been removed from the surgery team by Dr. Jackson Han, Shaun must use his talents to help figure out the cause of an infant’s injuries.

As a barroom fight sends Shaun to seek treatment at St. Bonaventure’s, Park and Lim disagree over an elderly woman’s post-operative symptoms. Melendez and Lim make their romance public, while Glassman continues to pursue a relationship with a good friend.