As the third season opens, the doctors of Chicago Med take their opinions to the extreme as they try to bring justice to the perpetrator in the shooting of Dr. Charles. Dr. Halstead and Dr. Manning work on a heart-wrenching case that forces them to examine their own matters of the heart. Though Robin's brain tumor was removed and she is discharged from the rehabilitation center, Dr. Rhodes remains on edge that her problems are not quite resolved. Meanwhile, Rhodes gets blindsided by his colleague Dr. Bekkar, Maggie sticks up for a patient and Dr. Choi and April try to navigate their new working relationship.
Dr. Manning goes to extremely measures to help a fearful pregnant woman whose baby is severely underdeveloped. April is angered by Dr. Choi when he uses their personal relationship as leverage to convince a patient of a risky procedure. As Dr. Rhodes attempts to balance his personal and professional life, it appears the stress of his current situation may have caused him to make a huge mistake. Dr. Charles and Dr. Reese continue to disagree about their psych patients.
When Goodwin receives financial complaints from the hospital board, she is forced to implement new guidelines that cause headaches for the doctors. Dr. Rhodes and Ava continue to compete in the operating room, while Dr. Charles and Dr. Reese are surprised when they treat a man who has a peculiar theory about his sickness. Dr. Manning and Dr. Choi can't figure out what is wrong with a young girl, leading them to look to a questionable source for answers.
Dr. Charles learns a troubling fact about the man who shot him. Dr. Rhodes and Dr. Bekker come to an agreement during a complicated surgery. Will and Natalie are trapped by legal ethics when an unfaithful husband refuses to tell his wife about his inconclusive Zika test. Meanwhile, April and Noah discover working together isn't always easy while Goodwin continues to argue with the board over hospital costs after an avoidable patient death.
When a young woman with HIV symptoms and no insurance refuses to take the test, Goodwin and Dr. Choi attempt to treat her without taking a toll on the hospital's resources. Natalie and Will try to diagnose a young girl with increasing paralysis. Noah deals with his first death as a resident and takes it upon himself to inform the family. Sarah continues to avoid work as her fear over the hospital's security increases.
Ethan attempts to diagnose a man with no symptoms while Sarah's paranoia goes to the extreme when she uses pepper spray on an aggressive patient. Will treats a young couple willing to sacrifice anything in order to have a baby. Meanwhile, Natalie must inform a woman that she was sterilized as a young girl without knowledge, and Goodwin and Maggie devise a way to persuade paramedics to bring in more patients.
Dr. Charles feels pressure when Dr. Choi and Dr. Manning criticize his medical decision regarding an ill newborn baby. Dr. Rhodes comes to terms with his relationship issues. Goodwin helps Bert understand Lyla's sickness.
Dr. Choi struggles to help a woman cope with anorexia. After a two-week suspension, Dr. Reese is immediately put to the test upon her return by Dr. Charles. Dr. Rhodes takes a stand when one of his patients is forcibly transferred. Meanwhile, Dr. Halstead is on a mission to get Dr. Manning's son to like him.
After discovering that a patient's family might have been abusive, Dr. Choi and April contemplate calling child services. Dr. Manning and Dr. Halstead struggle to see eye to eye in guiding a family who is dealing with their premature baby. Dr. Rhodes is persuaded into preforming a risky surgery on Dr. Bekker's mentor and world renowned surgeon, Dr. Marvin Jaffrey. Meanwhile, Dr. Reese joins Dr. Charles on a visit to the Cook County jail.
After witnessing a drive-by shooting and hitting her head, Dr. Manning struggles with the aftermath of a head injury. Complicating matters, she and Dr. Halstead deal with a teenage patient and her overbearing older husband, who might not be looking out for his young wife's best interests. Dr. Rhodes finds himself in a unique situation when he learns alarming information about the woman he went on a date with. Maggie is surprised to discover some unexpected things about the man she has been seeing. Dr. Charles is frustrated when Dr. Reese disobeys his orders and puts herself at risk.
After a neighbor is embraced, Dr. Choi enlists the help of April to figure out who is the real cause of the incident. Dr. Bekker and Dr. Rhodes expertise is put to the test when Noah misdiagnoses a patient. Dr. Charles is put in an uncomfortable position when Dr. Reese's estranged father comes to him as a patient without her knowledge. Meanwhile, Dr. Manning rushes to save a baby with whooping cough.
Upon hearing news of a pregnant teen, Dr. Manning and Dr. Choi venture to a homeless encampment to help deliver a baby under dire circumstances. Dr. Rhodes and Dr. Bekker argue about the best way to treat a young boy with a chronic disease. Dr. Halstead and April are put in an uncomfortable situation when they find out their patient is a pedophile. Goodwin and Maggie have to deal with a lawsuit against the hospital. Dr. Charles learns of important news pertaining to Dr. Reese's father.
Dr. Halstead and Dr. Manning are at odds over the care of a vegetative man; Dr. Rhodes goes behind Dr. Bekker's back to get his patient at the top of the transplant list; a woman in the waiting room falls asleep and won't wake up.
After a baby is abducted from Med, Goodwin enlists the help of Dr. Charles and Dr. Reese to find the suspect. Due to the lockdown, Dr. Rhodes must figure out a way to get into the operating room to help perform open-heart surgery. Dr. Manning and Dr. Halstead disagree on the right treatment for a patient.
Dr. Charles and Dr. Reese search for answers when a mother brings in her daughter claiming she is possessed. Dr. Rhodes and Dr. Bekker are tasked with finding a way to save a pair of conjoined twins. Dr. Halstead struggles to get Dr. Manning's attention. Maggie measures her options in the wake of her recent actions.
After taking the lead on a surgery, Dr. Bekker feels the heat after something goes wrong. Dr. Manning and Dr. Charles are faced with a tough decision concerning the gender of a 9-year-old girl. April and Dr. Reese rush to find the son of a dying patient. Goodwin's godson is admitted to the hospital.
After a 10-year-old boy is admitted to the hospital, Dr. Manning and Dr. Halstead disagree on how to best handle the boy's parents. Dr. Rhodes rushes to fix a heart that will be given to Dr. Reese's estranged father.
After a shooting occurs during a block party, the staff is overrun with victims; Dr. Choi devises a new mass casualty plan; Dr. Manning struggles to stay focused when she realizes her son and nanny might have been at the scene.
Dr. Manning rushes to save a young boy with a life-threatening case of the flu; April suspects Dr. Choi's sister stole opioid pain huggers; Dr. Rhodes and Dr. Bekker disagree over the best treatment for a cardiac patient who is 21 weeks pregnant.
Dr. Rhodes second guesses removing himself from the team working to separate conjoined twins; Dr. Choi and April make a startling discovery about his sister; Dr. Charles uncovers troubling information concerning Dr. Reese's father.