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. 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. 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.

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.

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.

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. 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.

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.

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. 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.

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 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, 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 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.

Dr. Claire Brown faces complications at home and work as she prepares to lead her first surgery. Meanwhile, a sports fishing accident challenges the rest of the staff as they look to treat the fisherman’s injuries without damaging his prize catch.

While performing his first solo surgery, Dr. Shaun Murphy alienates a nurse, which puts his residency in jeopardy. Dr. Neil Melendez disagrees with Dr. Audrey Lim on a risky surgery. Dr. Claire Brown spirals into self-destructive behaviors, causing negative ramifications in the workplace.

Despite everyone else’s doubts, Shaun is hopeful that Carly is truly fine with his friendship with Lea. The team treats a young boy born without a fully formed trachea and unable to speak, and who may be a good candidate for an experimental procedure.

Claire and Shaun treat a patient with a rare form of dwarfism. Reznick, Lim and Park treat a young man who had both arms torn off in a previous farming accident. Shaun reacts to an emotional situation.

In an effort to please Salen, Andrews takes on a high-profile case and assigns Shaun and Allen to help perform a risky surgery to restore the voice of a famous pop star.

Salen takes extreme measures when she learns that the surgical staff have joined Lim's efforts against her. The team treats a liver transplant patient whose organ donor unwittingly gave him cancer.

The team must deal with a mass casualty event that forces them to put aside their emotions following a recent tragedy.

Shaun, Jared and Charlie's young patient need his parents to agree on an important medical decision that could greatly improve his health; however, his parents are unable to agree on the correct path which spurs the team to try and intervene on behalf of their patient.