Rafe panics during a routine check by a local police officer and Steve is taking drastic measures that this won't happen again. Abby is not clotting properly and her baby has to be intubated.
Maggie arrives in Chicago to encourage Abby and Luka as their son's life is at stake. Sam is uncertain if her means to escape stay unpunished as act of self-defense.
On his first day as attending Pratt mostly has to deal with the new interns. An old man with congestive heart failure has to decide between his partner and his long-estranged family who didn't know about his sexual orientation. After he is not responsive anymore the two parties have different wishes for his further treatment.
As attending Pratt has to handle a busy ER. Morris is cheering for his biological son, who is playing in a soccer game.. Abby feels uncomfortable with the other mothers in her parenting class.
In trial Ames' attorneys try to prove that Kovac didn't pay enough attention to Ames' case back in 2004. Abby is back at work for the first day.
While treated for a motorcycle accident the drivers MRI pictures reveal an already metastasized tumor. A new nurse joins the ER staff. She is from New Orleans and worked there after Hurricane Katrina.
Abby and Luca are interviewing strange candidates who applied for babysitting baby Joe. Sam has to pick up Alex who is in custody of a supermarket manager as he was caught for stealing beer.
Abby and Kovac argue about a diagnosis when a woman comes into the ER with signs of spousal abuse. When a group of confused homeless kids enter the ER, Gates, Abby and Neela must quickly determine one child's ailment before it is too late. Meanwhile, Weaver is unexpectedly called to action while doing a news report at a school.
Abby is on helicopter duty for a huge bus accident.
Luka finds Curtis Ames spying outside the family's building, but doesn't tell Abby; the doctors help a young girl who may have been raped and work on a patient with an ice pick stuck in his ear; Pratt can't fully deal when his brother officially comes out.
Songs: Israel Kamakawiwo'ole -- Somewhere Over the Rainbow
Sam fights for a patient who is treated inhumanly by a different hospital. Dr. Barnett and Gates journey to the depths of the the city to help some homeless children. Dr. Morris gets a visit from a family member and turns a new leaf while Neela cares for a kidney transplant patient.
When a patient dies after being prescribed the wrong medication, Pratt and Hope question whether they are responsible. Meg comes to County General and angrily confronts Gates and Neela about their relationship. Dr. Kovac is forced to make budget cuts that could affect one ER doctor.
Luka reacts negatively when he sees Abby giving extra attention to a patient; Meg becomes infuriated when Gates moves out; Pratt is questioned by the police after one of his patients dies; Weaver makes a pivotal decision.
A desperate Ames steps up his quest for revenge against Kovac while Abby relentlessly tries to protect her family. At County, Sam has unsettling suspicions about the cause of the fire that set her home ablaze. As Sarah looks on, Gates and Neela attempt to resuscitate an unconscious Meg. Stuck in holding, Pratt has time to ponder his situation and his future.
Abby and Sam try to treat an obnoxious, aspiring comedian with mysterious symptoms. Pratt finds himself in hot water as he gets questioned about the death of a patient. Meanwhile, Neela is thrilled when Dr. Dubenko allows her to scrub in on a kidney donor surgery. In addition, Abby and Dr. Kovac decide to take their relationship in a new direction.
When a woman comes into the E.R. with acute liver failure, Gates and Kovac find themselves with a moral dilemma. Neela also questions what is right when Manish decides to give up a kidney for a complete stranger. Meanwhile, Ray fights to get to the bottom of a cheerleaders accidental fall.
Abby and Pratt quickly try to save a family suffering from frostbite after getting stuck in the snow. Neela gets jealous when Dr. Dubenko brings in a new surgical intern. Meanwhile, Gates struggles with the reappearance of his dad and the possiblity of losing Sarah.
The ER doctors treat the victims of a car vs semitrailer accident. A photographer gives Sam a different perspective on life. Morris and Hope are overzealous in their attempts to help Luka and Abby with their wedding plans. Neela and Ray try to sort their relationship out. Gates uses a medical student to take care of his paperwork for him.
Kovac and Abby acclimate to their new roles as husband and wife; Hope and Morris enjoy the honeymoon suite; Pratt hopes to win over a new woman; a new doctor (Stanley Tucci) in the ER means business.
In the 13th-season finale, Kovac leaves his new bride and ER staff in the hands of a new chief bent on change while he visits his ailing father back in Croatia. Meanwhile, Neela puts herself in a life-threatening situation when she attends an antiwar rally; and Gates has to leave work when Sarah panics about her future.