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.

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.

Following his father's death, Shaun must deal with the effects his intimacy with Lea will have on his relationship with Carly; the team operates on a patient who is refusing all anesthesia during surgery for fear of relapsing.

Dr. Shaun Murphy questions his decision to give the new residents autonomy when one of his intern's misdiagnosis of a patient has dire consequences. Meanwhile, Dr. Claire Browne, Dr. Alex Park and Dr. Jordan Allen treat a patient with a ruptured cyst affecting key functions of her brain. And elsewhere, Dr. Morgan Reznick and Park bond over failed relationships.

When a renowned surgeon comes to St. Bonaventure for treatment, the team’s enthusiasm is quickly overshadowed by the doctor’s behavior. After studying his case, Dr. Shaun Murphy sees a pattern he recognizes. Meanwhile, Shaun and Lea are forced to make a life-changing decision that will alter the course of their relationship.

Shaun and Lea happen upon a terrible car accident and discover a young pregnant mother who has been badly injured and needs immediate medical attention. Dr. Glassman is apprehensive when a figure from his past reaches out for help.

When someone mistakenly brings a hallucinogen-laced dish to the hospital's company potluck, much of the hospital staff and doctors are incapacitated -- leaving doctors Murphy, Glassman and Allen forced to take on all the hospital's cases, further exacerbating Dr. Murphy and Dr. Glassman's conflicting work styles.