Lim is challenged by the unique circumstances surrounding a pregnant patient with an aggressive tumor. Elsewhere, after misdiagnosing a patient, Claire makes a disconcerting discovery about certain practices at the hospital.

Dr. Shaun Murphy is surprised to learn that his young cancer patient identifies as a girl while being biologically male. Shaun must quickly learn to understand his patient, her medical needs and how to work with her family, who all feel they know what is best for her.

Carly’s attempts at increasing her intimacy with Shaun are becoming more of a frustration than either of them expected. Meanwhile, Lim and Melendez struggle in their relationship as they work to separate their work from their personal life.

After finding out the gender of their unborn child, Lea's enthusiasm prompts Shaun to make an effort to be a more supportive partner. Meanwhile, the team treats a navy pilot whose previous doctor's misdiagnosis compromises her chances at a full recovery.

Dr. Shaun Murphy's teenage patient has been confined to her home her entire life due to a rare heart condition. Despite her condition, she has cultivated a large group of friends online and hopes that the surgical team can find a way to give her the life she has always dreamed of having. Meanwhile, a young patient's perfectly matched organ donor is causing a moral dilemma for the parents and the patient.

Dr. Murphy treats a patient who has an illness that is not only unpredictable in nature, but also unlike anything he or the team has seen before. Dr. Claire Brown continues to work through her grief, still reeling from Dr. Neil Melendez's death.

Dr. Shaun Murphy suspects his patient is lying about the reason for her injury and makes a controversial assumption about her motives. Meanwhile, Dr. Neil Melendez’s personal life could be affecting his work and, ultimately, his patients lives.

Dr. Shaun Murphy proposes a radical surgery to save a woman's life after what he believes was a disastrous first date with Carly. Meanwhile, after the new chief of surgery, Dr. Audrey Lim, announces that the residents can lead surgeries, Dr. Morgan Reznick and Dr. Alex Park compete for the chance to operate on an elderly patient who has been diagnosed with cancer.

Dr. Shaun Murphy’s unique ability to relate to a patient isolated by an immune deficiency yields an unexpected result. Meanwhile, Dr. Claire Browne, Dr. Morgan Reznick and Dr. Marcus Andrews treat a 12-year-old patient who is about to become blind, and tension builds between Dr. Neil Melendez and Dr. Audrey Lim.

With several candidates vying for residency at St. Bonaventure, Chief of Surgery Dr. Audrey Lim tasks Dr. Shaun Murphy, Dr. Claire Browne and Dr. Alex Park with mentoring the top first-year resident contenders. As their mentees shadow them for the day, Shaun and Park meet with Andrews to discuss a difficult surgery scheduled for a minor. Later, Shaun inadvertently insults Lea while discussing the pros and cons of the controversial surgery. And elsewhere, Dr. Morgan Reznick seeks out Claire and Lim’s help on a consult.

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.

As part of St. Bonaventure hospital's international humanitarian program, the team takes on the case of a young boy from the Congo who has severe congenital heart anomalies. Dr. Neil Melendez has doubts about the safety of the procedure, while Dr. Shaun Murphy works out the best course of action. Meanwhile, Murphy's latest encounter with his neighbor Lea has him confused.

Dr. Claire Brown and the team must face hard truths about what lines they are willing to cross when one of Claire's idols becomes her patient.

Shaun and Lea go on a camping trip to distract themselves from their grief over their miscarriage. Meanwhile, Morgan and Park argue about the best course of treatment for their patient.

When the team treats a patient who has to decide between a dangerous surgery that could change his life or remain the same, he asks Dr. Shaun Murphy what he would if he had that same choice.

Dr. Shaun Murphy and Dr. Morgan Reznick must contend with two brothers who are bargaining over life and death. 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. Neil Melendez and Dr. Jared Kalu discover their patient isn’t being completely honest with them which may cost him his chance at a life-saving surgery. Meanwhile, Dr. Claire Browne must learn to communicate with Dr. Shaun Murphy as they race back to St. Bonaventure Hospital with a donated organ.

Dr. Marcus Andrews enlists Dr. Neil Melendez on a very sensitive kidney transplant between a pair of twins; Dr. Shaun Murphy decides to take an impromptu trip with his friend Lea and leave his problems behind.

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, 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.

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 their friendship and roommate status.

As a conspiracy theorist questions Dr. Neil Melendez’s diagnosis, Dr. Claire Brown treats a woman whose inability to feel pain is threatening both her marriage and her life. Meanwhile, Dr. Shaun Murphy and Dr. Aaron Glassman each face crises in their romantic relationships.

Dr. Shaun Murphy has been assigned his first surgery by Dr. Audrey Lim. However, Dr. Marcus Andrews questions whether he is really ready. Meanwhile, as Dr. Claire Brown continues to avoid her complicated emotions about her mother, she and Dr. Morgan Reznick have a patient whose diagnosis has them doubting his story.