Gates is assigned to the case of a closeted gay man whose partner clashes with his family; Neela meets her new surgical chief, Dr. Crenshaw; and Pratt must cope with the flood of new interns.

Abby and Kovac discover both the joys and difficulties of raising a newborn; Morris is wrongfully accused of being a child molester; Pratt has his trial-by-fire when he has to handle the ER alone, juggling multiple traumas, teaching duties and a troublesome intern. Neela continues to be the target of her difficult supervisor, and Sam discovers her sons latest extra-curricular activity.

Kovac anxiously awaits the verdict between himself and Curtis Ames but fears the worst. Meanwhile, Neela disobeys her chief's orders and also questions her feelings for Gates, and Weaver unwittingly steals the spotlight from Morris in his big television debut.

A mysterious illness leaves little hope when a group of homeless kids enter the ER and one of them believes that Neela is a guardian angel in blue; Abby and Kovac clash over a possible case of domestic abuse; Pratt makes a shocking discovery about his brother, and Weaver is unexpectedly called into action when her television appearance becomes a real emergency.

Thanksgiving at County is quiet, with the normal number of routine (or nearly so) emergencies. But Abby makes up for the lack of excitement while returning to the hospital as the doctor on a helicopter transport.

Weaver cares for a Katrina survivor who's reluctant to have surgery on her foot; budget cuts force Luka to make a difficult personnel decision. Also, Gates' home life intrudes on the ER; and Pratt and Hope are shaken after a patient in their care dies needlessly.

Kovac reacts negatively when he sees Abby giving extra attention to a patient; Ray and Gates clash over a patient, pinning Neela in the middle; and Ben takes things to the next level with Sam. Meanwhile, Pratt is under investigation and Weaver says a final goodbye to the ER.

Kovac finds himself in a tense confrontation with Curtis Ames, and Abby must act to protect her family. Meanwhile, Neela and Gates rush to get Meg to the hospital while Sam's new home is soon under threat from fire.

Abby and Sam try to treat an aspiring comedian with mysterious symptoms; Pratt must defend his actions in front of the medical board; Neela scrubs in on a kidney donor transplant; and Morris, as the lone attending, must run a busy ER. Also, Kovac gets a surprising proposal from Abby.

Kovac and Gates find themselves with a moral dilemma when a woman comes into the ER with acute liver failure; Neela finds herself questioning what is right when Manish decides to give up a kidney to a complete stranger. Meanwhile, Ray fights to get to the bottom of a cheerleader's accidental fall; Abby gets a prediction for her future; and Alex's troubles continue to intrude on Sam's work life.

A blizzard strands a family in the snow and Abby and Pratt quickly try to save the family. A gang shooting challenges Morris and Pratt. Meanwhile, Kovac and Abby begin making wedding plans, but their engagement might not be very secret; Gates struggles with the reappearance of his father and the possibility of losing Sarah; and Neela becomes jealous when Dubenko brings in a new surgical intern.

It's Sam's birthday, but she finds it hard to be away from her son Alex. Meanwhile, Sam meets a photographer taking pictures of a terminal patient and she gives Sam a new perspective on life. Dubenko's new surgical intern unsettles Neela during a trauma; Gates is shadowed by a new and nerdy intern and later must tell Sarah the truth that he may be her biological father. Also, Morris and Hope annoy Kovac and Abby when they try to help with their wedding preparations.

Kovac and Gates deal with a hopeless father whose son succumbs to heart failure; Pratt tries to resolve the tension between him and his brother; an Armenian man tries to be a good samaritan but ends up crashing near the ER; Abby sneaks in baby Joe when she worries his sickness may be worse than it seems; Also, Sam injures the instructor of a self-defense seminar.

In 12 hours, the ER will shut down. As Kovac is under pressure to take care of the patients before the final hours, he makes a pivotal decision about his future. Meanwhile, Sam befriends a photojournalist who returns only this time she's terminally ill; Pratt is concerned when his brother ends up in the ER drunk; Morris confronts Gates when he ignores his orders and angrily sends him home while Gates tries to defend his actions.

The ER reopens with new changes. However, the ER is not the only thing that's changed; Kovac and Abby adjust to being newlyweds; Morris and Hope enjoy themselves at the honeymoon suite; Pratt attempts a change for a woman; Neela worries when Ray goes missing; Meanwhile, there's a new doctor in the ER and he means business; and another change may come when Kovac receives a phone call.

The ER is now in the hands of a new chief, Dr. Kevin Moretti, who is bent on major changes. Meanwhile, a phone call leads Neela to a hospital where a major shock awaits her, and a final farewell from a friend and colleague. Gates urgently goes home to stop Sarah from being taken away from him. A drug-addicted Iraq War veteran baffles Morris and Sam. Also, Kovac postpones the honeymoon and says goodbye to Abby and his son, for the meantime, while he travels to Croatia to visit his ailing father.

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.

Gates and Julia nurture their newfound romance but are soon interrupted by a troubled phone call from Gates' ward, Sarah.

Dr Wexlar is made interim ER chief while staff deals with an industrial accident that leads to a hate crime.

Neela's marathon shift begins to affect her, and her demeanor isn't helped when she learns the med student she is mentoring is abandoning her specialty.

When a thirteen-year-old gymnast is brought into the hospital after having supposedly fallen off a wall, Dr. Banfield and Dr. Gates must sort out whether abuse is involved.

A woman who broke her leg while trying to escape a house fire is brought in with her husband. The husband, Mr. Lotery did not let the paramedics to check him over. Then his brother-in-law arrives, saying that he predicted that something like the house fire would happen - it was actually an arson. Mr. Lotery's brother-in-law becomes aggressive and accuses him of being a pervert, specifically a pedophile. Mr. Lotery denies the accusations. He was sued but found not guilty. When Mr. Lotery is waiting for his wife who's in line for X-ray, he has the chance to calm down a young girl who is afraid of needles. When his brother-in-law sees this, he brutally assaults him, while Dr. Brenner calmly watches nearby... Meanwhile, Neela gets sued for malpractice.

As a snowstorm hits Chicago, Sam's son Alex crashes a car and ends up in critical condition in the ER. Neela gives a deposition in the malpractice suit against her. Dr. Morris and Dr. Banfield are both at a medical conference in Omaha, and when the snow cancels all flights out they share a memorable and surprising evening.

As Carter prepares to open a new facility for the underprivileged, some old friends/colleagues gather. Rachel Greene, Mark Greene's daughter, applies for an internship at County.