Emily learns that the nurses don't like her when she is assigned a difficult case as revenge. Later, Emily reveals her feelings to Will, and considers using a secret she knows about the chief to get a speedy approval on a procedure.

Emily talks about safe sex to some girls at a local high school; and she tries to forget about her feelings for Will.

Emily and Micah are frantic when they discover their patient needs a kidney transplant immediately, but they are baffled when she mysteriously refuses to accept the kidney from her new husband. Elsewhere, Emily assists Dr. Hamada (Brittany Ishibashi) and Dr. Bandari, with a risky surgery after they discover that one of the babies their patient is carrying for her sister suffers from a defective heart valve. Meanwhile, in an effort to keep Cassandra away from Will, Emily tries to land the job as Dr. Bandari’s research assistant. However, her competition is Cassandra, who is willing to play dirty in order to get what she wants.

Emily suffers a major embarrassment in front of her colleagues at the hands of a drug-impaired patient. In the aftermath, Emily decides to follow Dr. Bandari's advice and tries to toughen up. Emily and Will find that a teenage patient needs a partial liver transplant, but they uncover some surprising information when neither of the teen's parents is a match. Meanwhile, Cassandra starts treating Emily better in an effort to learn more about Will, and Tyra sets Emily up on a date with her ex, a fact which she doesn't reveal to Emily.

Emily treats an infant and a deeply religious man whose faith is shaken following surgery. Meanwhile, Will breaks protocol with a risky diagnosis; and Tyra considers telling her father that she is a lesbian.

A beloved flower-delivery man collapses, but he is reluctant to get treatment. Meanwhile, Emily and Will are assigned to help a sick prisoner, but they find it difficult to remain professional and not let his crimes cloud their judgment.

When a female car accident victim is brought into the ER with a spike through her torso, everyone immediately blames her boyfriend for causing the accident. She makes it through surgery, but the doctors find that she may be paralysed. Later, they discover that the boyfriend has lupus, which could be to blame for the accident. The case brings up painful memories for Will. Emily deals with a model with jaw cancer who refuses to undergo surgery. Emily and Cassandra compete for Will's attention as they all prepare for the in-service exam.

A man gets admitted in a costume and claims to be King Paravel from the Elvish nation. The man later goes blind which leads Will to believe he is suffering from conversion disorder, a psychiatric problem. Emily refuses to jump to conclusion so quickly. Another patient is a woman diagnosed with cancer who later passes away due to an unexpected cardiac arrest. Her upset daughter sues Micah for medical malpractice. In an attempt to prove that she is not predictable, Emily agrees to let Tyra dress her up for a blind date arranged by Cassandra. Emily shows up to the date beautifully which later causes Will to act jealous. Micah realizes his true feelings for Kelly. Doctor Bendari realizes she has been putting career before life and attempts to change it.

After a year long absence, Dr. A.J. Aquino returns to Denver Memorial, but before he can rejoin the staff, the Chief insists that he make peace with Dr. Bandari. Emily is tasked with treating a patient who claims to be a psychic, and is convinced that her tarot cards predict her own impending death. Elsewhere, Cassandra and Dr. Bandari treat a patient who needs a lung transplant, but Micah’s discovery of a new medical issue leaves the patient with a tough decision. Meanwhile, Emily decides to test her theory that Will was jealous of her recent date, so Tyra offers to teach Emily how to flirt.

When Emily, Will and Cassandra compete against each other to be Dr. Bandari's research assistant, feelings get hurt when they have to describe each other's flaws. Emily is determined to solve the medical mystery of a young patient whose x-rays reveals a bullet lodged in his lung, but who has no signs of a gunshot wound or scar. Meanwhile, Emily comes to a revelation about her personal life after diagnosing a daredevil with a rare disease that forces him to change his entire life.

When the hospital is inundated with bus crash victims during a winter storm, Emily is assigned to run triage in the E.R. During the chaos, Emily is forced to do an emergency skull procedure on a heroic Marine who suddenly collapses. Tyra bristles at her father’s lack of respect for her as a doctor, but they later experiences a breakthrough when they perform an emergency c-section together. Meanwhile, Will and Emily secretly work to help an unexpected patient leaving Cassandra to question Will’s true feelings for Emily. Micah finally makes a bold decision in his personal life.

Season Finale: Emily's decision about starting a relationship with Micah becomes even more complicated when Will hears about it and begins to feel jealous. Emily and Tyra treat an unruly woman, but after learning of her home hoarding situation, Emily wonders if the woman's personality changes may be caused by her many cats. Now that Cassandra and Will have broken up, Cassandra's strictly professional behavior distracts Will and causes him to misdiagnose their patient. Meanwhile, Micah's sister comes to town after finding out the truth about their mother.