The team at St. Bonaventure needs to quickly discover the truth behind a young college student’s unexplained injuries before his condition worsens. Meanwhile, after losing his most prized possession, Shaun’s distraction during a surgical procedure may end up risking more than just his job.

Dr. Shaun Murphy, a young surgeon with autism and savant syndrome, relocates from a quiet country life to join the prestigious St. Bonaventure hospital’s surgical unit. Alone in the world and unable to personally connect with those around him, his only advocate, Dr. Aaron Glassman, challenges the skepticism and prejudices of the hospital’s board and staff when he brings him in to join the team. Shaun will need to work harder than he ever has before, as he navigates his new environment and relationships to prove to his colleagues that his extraordinary medical gifts will save lives.

While in the exam area of St. Bonaventure Hospital, Dr. Shaun Murphy encounters a young patient who looks eerily similar to his deceased brother, Steve. After discovering his parents have hidden his diagnosis from him, Shaun struggles to understand why he doesn’t deserve to hear the truth about his own health. Meanwhile, the team can’t figure out what keeps triggering their patients’ increasingly severe allergic reactions and races to find the cause before the next one kills another patient.

Dr. Shaun Murphy and Dr. Claire Browne devise an experimental procedure that can save the leg and life of a young groom, that is if his bride-to-be and parents can learn to work together. Meanwhile, Jared struggles to emotionally connect with his patient whose scars may prove too deep to overcome.

Dr. Shaun Murphy has to confront prejudice from an unlikely source when he takes on the case of a patient with autism, and Dr. Jared Kalu has to learn to accept his limitations as a surgeon.

Dr. Shaun Murphy’s attention to detail complicates his first day at St. Bonaventure Hospital. Meanwhile, Dr. Claire Browne learns a valuable lesson about honesty when confronted with a difficult diagnosis for her patient.

During a robbery at the grocery mart Dr. Shaun Murphy is shopping at, his communication limitations puts lives at risk. Meanwhile, after Shaun's traumatic day, Dr. Aaron Glassman worries that he isn't doing enough to help Shaun.

A charming young doctor puts a member of the surgical team in an awkward position at work; Dr. Glassman suggests that Dr. Shaun Murphy meet with a therapist.

Dr. Shaun Murphy questions the need for an elective surgery that will allow his young patient to smile for the first time. Meanwhile, Dr. Claire Brown and Dr. Morgan Reznick discover that their patient lied about her identity.

The twins suffer complications from their surgery forcing the team at San Jose Boneventure Hospital to make a life-changing decision. Meanwhile, Dr. Shaun Murphy returns to the hospital after his trip with Lea and decides he needs a more permanent change and gives Dr. Aaron Glassman his two weeks’ notice.

Dr. Neil Melendez and the team have to wade through legal waters when a husband and wife have to make a life-changing decision about their unborn child. Meanwhile, Dr. Shaun Murphy struggles to adjust to his new environment at home and makes a huge step forward with his colleagues.

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 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.

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. 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'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. 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.