Last season all kind of crazy happened at San Jose St. Bonaventure Hospital, Andrews, now president of the hospital, Glassman beginning his cancer treatment, Claire coaches Shaun on how to ask a woman out, Lim and Melendez are date and more.
Andrews starts by shaking thing up by telling Shaun to learn to communicate, Claire to be more assertive, and Morgan to improve her teamwork. Jared, working his last day before moving to Denver. Glassman is having a tough time with is diagnosis and Jared advice Shaun to spend time with Glassman, who is beginning his cancer treatment. Which lead Shaun to diagnose Harry with a brain tumor as well as helping him within persuading to receive treatment and reunite with his family. Claire has a change of heart and asks Jared to stay, but he tells her they will both be happy apart before leaving for Denver and Lea returned.
Shaun and Claire assist Dr. Melendez in treating Paul, a hospital janitor Shaun was diagnosed with pancreatic cancer and one year to live. Dr. Lim treats Mara, a sixteen-year-old American girl with scarring from female genital mutilation, risking liability in willfully ignoring Mara's fake ID. Lim performs the reconstruction without consent after experiences extreme pain, revealing live tissue. Dr. Glassman delays picking a neurosurgeon, fearing he could survive but suffer permanent disability but later got surgery. Shaun is having a hard time being around Lea and avoids her but later tells Lea she hurt him, and he wants her to leave before she hurts him again.
The new chief of surgery is here and ready to scrub in.
Tensions rise among Melendez, Claire, and Nurse Flores When a risky procedure is the only way to avoid a hysterectomy, the patient's husband refuses to decide; he cedes the responsibility to Claire, who overrides Melendez's decision they perform the hysterectomy and Dr. Andrews got involved. Shaun and Morgan safely extract a light bulb from a child's mouth and treat a young man whose priapism reveals an abscess.
After sleeping together, Drs. Lim and Melendez agree not to do so again despite both having enjoyed it. The ER and its waiting room are quarantined after two patients, travelers returning from Malaysia, die of a viral respiratory disease. Those quarantined include Shaun, the aftermath of the quarantine, the governor orders a review of the hospital; the investigator expresses concern about Andrews maintaining his dual role and recommends Shaun, Lim, and Melendez to the medical board for license suspension over their actions. Glassman decides to speed up his treatment after a fun day while Shaun learns that Lea has a boyfriend.
Glassman completes his chemotherapy and attempts to renew his relationship with Debbie. However, hurt by Glassman pushing her away while he was sick, Debbie rebuffs him. Shaun is demoted to pathology by Dr, Han against his wishes. Han stating who is unimpressed with Shaun bedside manner tells him that he would do good in pathology and he can save patients without interacting with them.
After Shaun saves patient Han publicly credits Shaun as the pathologist who saved a grateful Sadie's life. Shaun requests his old job back, but Han presents Shaun's unique ability to correctly diagnose Sadie as proof that Shaun belongs in pathology.
Glassman's final test results show that he is completely cancer-free. Han meets with the medical review board regarding the events of the quarantine resulting in the hospital will pay some fines and Shaun, Lim and Melendez will have to attend a few classes, and everyone else was cleared.
Shaun is still stuck in pathology. A patient with a 200-pound tumor encircling his body. When complications arise, Melendez insists on bringing in Shaun to consult; Shaun comes up with a plan to complete the operation safely, the surgery is a success. Later Shaun had an emotional breakdown and demands his job back from Han in a way that leads to Han firing him. Lim decides to make her relationship with Melendez public and goes to Andrews with him.
In the season finale, At the risk of his career, Andrews fires Han and rehires Shaun. Glassman proposes to Debbie; she declines, but later said yes. With some coaching from Claire, Shaun asks Carly out; she says yes. Lim and Melendez make their relationship public, but thing becomes complicated as they are both up for the Chief of Surgery position, which quickly lead to a breakup. They agree neither of them should decline the position; Melendez reveals he already knows Andrews has chosen Lim.
The first three episodes are "Disaster”, "Debts" and "Claire" base on the title all I can say is “ I can’t wait for tonight premiere.”