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.
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.
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. Meanwhile, a young patient must decide on a treatment that could save her life or possibly destroy her marriage.
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.
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.
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. 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.