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. 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'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. 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.

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 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.

Shaun visits his father on his deathbed and the family reunion reveals unexpected results. Melendez, Park, Reznick and Claire treat an injured star NFL player with severe spinal damage. Claire addresses her mental health.

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.

When the hospital is hit with a cyberattack threatening to shut down life-saving machines, Lea rises to the challenge and looks to outsmart the hackers to prove herself. Meanwhile, the team treats an inspirational cancer survivor-turned-successful-philanthropist who harbors a dark secret.

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.

Shaun confronts Salen about the many changes she has implemented since coming on at St. Bonaventure. Glassman is forced to accept his new role at the hospital.

Now that Shaun has called off the wedding, he is forced to confront Lea about their relationship and determine what he really means to her. Meanwhile, the team debate their opinions on plastic surgery and Dr. Audrey Lim hopes to expose Salen’s cover-up over an infant’s death to take her down before it is too late.

The team operates on a military reenactor whose attempt at authenticity has created an explosive predicament that even Dr. Shaun Murphy couldn’t predict. Meanwhile, Dr. Jordan Allen and Dr. Daniel Perez are on a race against time as they search for a severed foot.

Shaun invites Aaron to stay with him while he has exterminators at his house and Lea realizes both men have a lot more in common than she realized. Meanwhile, Dr. Morgan Reznick wrestles with a big decision about her career and her personal life.