Abby, Pratt and Morris clash with Moretti's strict new ER procedures as victims of an anti-war rally roll in, including Neela. Gates manhandles a patient he suspects set off the explosion that disrupted the protest. A worried Dubenko lets his emotions for Neela take over during Neela's surgery. Meanwhile, the rest of the staff worry over Neela's condition.
Patients include a pregnant teacher whose student/lover was critically injured while driving; a man who is hiding a gunshot wound and a brilliant young boy who knows he is dying, but hides it from his mother. Dr. Moretti continues to remake the ER to his liking, Neela is recovering, Luka's absence is reinforced (back in Croatia and not coming back) and Sam may be starting a new relationship with a police officer.
Abby and a distracted Morris work to save two auxiliary cops brought in with gunshot wounds. Pratt treats a teen wrestler with severe vomiting, but the problem is much more serious. Sam worries over her new beau Litchman. Gates tries to help a young boy in the ICU with a deadly disease. Also, Dubenko visits Neela while she babysits baby Joe.
Moretti reassigns Gates back to the ER and treats a couple involved in a car accident. Morris prepares to take his written board exams. Neela is assigned a young genius intern. Kovac plans to extend his stay in Croatia while Abby struggles with single parenthood.
Moretti brings in new attending Skye Wexler to help with the patient load. Morris and Pratt cram for the medical board exam. Gates treats a returning patient from the ICU whose condition has worsen. Sam tends to a teenage girl who is feeling neglected by the staff. Neela's intern, Harold, seeks her advice on a personal matter. Abby struggles with her relapse.
The city suffers power outages during an unseasonably hot spell. Nursing-home patients are brought into the ER suffering from hyperthermia. Abby and Pratt disagree on the diagnosis of a fussy baby. Abby falls back to old habits and quickly down spirals to rock bottom on a night she'll forever regret.
Morning shift begins. The night shift treated 142 patients - a new record. Dr. Morris is confident that by the end of the day the ER can set a new record of 300 patients. Frank reminds him that there has never been more than 250 patients in a day. Dr. Morris bets $300 that they can reach 300 by the end of the shift. Frank, Dr. Gates and Dr. Pratt each bet $100 against him. But will the game be fair? Also, when chaplain Dupree arrives announcing that she's doing a round of the hospital, holding blessing ceremonies and memorials, the guys are against it, except for Dr. ...
Dr. Pratt applies for the job of ER Chief and gets turned down. This causes him to give 2 weeks notice. A female soldier, home 2 weeks from Iraq, is 2 months pregnant and her husband demands an explanation. Neela's cousin has arrived from London for an extended visit and gets pursued by both Dr. Morris and Harold Zelinsky. After 9 years absence, a fall in gym by her son brings Jeanie Boulet back to the ER. Not only is she troubled because of her son, but the disorientation of knowing virtually no one on the current staff does not help.
A firefighter is brought in after being injured at a fire that is blamed on a young girl with genetic problems. Abby decides to prove the girl did not cause the fire. A disfigured man saves his anti-social neighbor. An old woman dies unattended at the ER while the staff are waiting for a psychiatrist. Pratt backs up Abby in an administration meeting. Neela's cousin apparently chooses Harold.
A young couple is choppered to County after a car accident, and one of them has a gun. A boy who wants to be a clown is injured in a unicycle mishap, but his father considers him a mathlete and wants him to go to MIT. Pratt visits Bettina in the hospital, but she tells him off.
In the season finale, an ER patient with a mysterious past is afraid that people are trying to kill him. Dr. Moretti returns, trying to make amends for wrecking the marriage of Abby and Luka. Neela makes her way through a difficult M&M conference. Morris treats a woman with lupus who has an attractive daughter.