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

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

Dr. Melendez, Dr. Brown and Dr. Park have given a young married couple two choices about their future: save the wife's life or their future ability to start a family. Meanwhile, when Dr. Lim has to take care of some personal business, she leaves oversight of the emergency room to Dr. Murphy and Dr. Reznick; and Dr. Glassman's post-op recovery leaves him struggling to get the rest he needs for recovery and also confronting his relationship with his daughter.

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.

When a patient suffering from anorexia can't gain the necessary weight needed to survive heart surgery, Claire suggests they perform an experimental surgery which Melendez strongly opposes. Shaun worries Glassman's refusal to walk the hospital floor will keep him from being discharged and tries to persuade him to ambulate. Meanwhile, Shaun and Lea change the terms of their current relationship.

Morgan and Shaun's indecision on how to treat a young violinist who visits the ER with an infected finger could affect her future in more ways than one. Meanwhile, Lim, Claire and Park can't figure out if their young patient is really ill or looking for attention.

Dr. Shaun Murphy and Dr. Morgan Reznick must contend with two brothers who are bargaining over life and passing. Meanwhile, Dr. Claire Brown's friend who is dying of cancer asks her for something she doesn't think she can give her; and Dr. Aaron Glassman is dealing with the effects of his treatment.

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. Audrey Lim 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.

The hospital is still in quarantine as Dr. Murphy continues to be overwhelmed by the chaos and noise in the emergency room; Dr. Reznick struggles to keep her patients alive, and Dr. Lim fights for her life.

In the aftermath of the quarantine, the staff tries to return to their normal routines. Meanwhile, as Dr. Lim recovers from the virus, she and Dr. Melendez navigate their new personal and working relationship, while Dr. Murphy and Dr. Glassman visit Lea.

Dr. Shaun Murphy, Dr. Morgan Reznick and Dr. Audrey Lim treat a woman with autism and a delicate brain condition while navigating the complicated relationship she has with her roommate, who is also on the spectrum. Meanwhile, Lea and Shaun are still figuring out.

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 by Dr. Jackson Han from the surgery team, he must use his talents to help figure out the cause of an infant's injuries.

As a barroom fight sends Dr. Shaun Murphy to seek treatment at St. Bonaventure's, Dr. Alex Park and Dr. Audrey Lim disagree over an elderly woman's post-operative symptoms. Meanwhile, Dr. Neil Melendez and Dr. Lim make their romance public, and Dr. Aaron Glassman continues to pursue a relationship with a good friend.