Following what he believes was a disastrous first date with Carly, Dr. Shaun Murphy proposes a radical surgery to save a newlywed woman's life. 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.

As Dr. Marcus Andrews vows to help a good Samaritan who was injured while stopping a sexual assault, Dr. Audrey Lim faces a difficult decision when a young patient's parents suspect that Dr. Neil Melendez made a mistake. Meanwhile, Dr. Shaun Murphy fields advice following his disastrous date with Dr. Carly Lever; and Dr. Claire Browne gets a surprise visit from her mother.

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.

As a conspiracy theorist questions Dr. Neil Melendez's of his liver damage, 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.

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

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.

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.

Shaun is ready for the next step in his relationship with Carly. However, he continues to struggle as they grow closer and more intimate, and is dealt some troubling news about a deeply personal issue. A young patient must decide on a treatment that could save her life or possibly destroy her marriage.

Shaun visits his father on his passingbed 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.

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

Dr. Audrey Lim, Dr. Shaun Murphy and Dr. Morgan Reznick treat a 25-year-old runner suffering from severe swelling; but when things take a turn for the worse, Dr. Shaun Murphy enlists the help of Dr. Carly Lever. Meanwhile, Dr. Alex Park, Dr. Claire Browne and Dr. Neil Melendez treat two 16-year-old cancer patients who are dating; and Dr. Shaun Murphy and Dr. Carly Lever work toward intimacy.

Dr. Shaun Murphy and Dr. Morgan Reznik grapple with a terminal cancer patient who is determined to live the last few months of his life without inhibition. Meanwhile, Dr. Reznik must confront her relationship with her mother when she comes in for a third opinion from Dr. Glassman; and Shaun and Carly's relationship reaches a new level of intimacy.

After Shaun treats a patient who is a social influencer, he deals with unwanted attention. The team treats a woman who is in abdominal distress after an at-home faecal transplant Carly's efforts to separate Shaun from Lea are challenged.

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.

When Dr. Shaun Murphy makes an emotional confession, the result may not be as desired. Meanwhile, he becomes obsessed with performing an autopsy on a Jane Doe, which challenges his relationships at the hospital; and Dr. Claire Browne, Dr. Morgan Reznick and Dr. Marcus Andrews treat a male college student with a mysterious split personality disorder.

A patient with a mysterious and undiagnosed illness that has baffled other doctors for years forces Dr. Shaun Murphy and the team to take some big risks. Meanwhile, Dr. Claire Brown and Dr. Neil Melendez continue to cautiously navigate their feelings for each other as colleagues and friends.

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.

The city of San Jose is rocked by a massive earthquake that puts the staff of St. Bonaventure Hospital on high alert as they race to assess the damage and account for the safety of their colleagues and friends. Meanwhile, Dr. Neil Melendez and Dr. Aaron Glassman are attending a charity event when their lives are threatened by the earthquake.

The doctors work against time and their own personal safety to save the lives of those around them.