The hospital staff copes with the immediate aftermath of the shootout. Weaver finds Abby unconscious and Kovač tied to a gurney. Abby's trauma puts her into pre-term labor, and when the risk of placental abruption becomes a reality, her baby is born two and a half months prematurely. When bleeding continues, Abby undergoes a hysterectomy. Jerry's heart was nicked by a bullet and he has to have surgery, which Dubenko and Neela perform successfully. After a rough chase from local police, Steve and his co-conspirators decide to hide out with hostages Sam and Alex. Eventually Steve shoots both of the co-conspirators, who want to dump Sam and Alex, and then tells Sam that he would rather his family were all dead than to be separated again. Later that night, after Alex is asleep in the van, Steve rapes Sam. When Steve falls asleep, Sam takes the keys to the van and prepares to escape with Alex but then goes back, picks up Steve's gun, and shoots him three times.

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NOTE: This is the first episode until the series finale that does not feature the original opening title sequence or James Newton Howard's theme song.

While Abby's baby, Joe, struggles in the NICU, Maggie visits and has a more pleasant time than usual with Abby. Sam's former employer, Elliott, helps her forestall any police investigation of Steve's death. Pratt becomes an ER attending. Kovač and Abby clash about trying a risky experimental treatment for Joe; eventually Abby agrees and Joe improves, but develops complications that are noticed at first by Maggie, who insists that the Attending, Dr Rabb, be paged, saving baby Joe's life. He requires surgery, but finally recovers. The hospital board meets to fire Kovač over the Clemente fiasco; when Weaver confesses that she, not Kovač, was responsible, she is demoted to an ER attending. Morris is disenchanted as a pharmaceutical representative and wants, and finally gets, the open ER attending slot, with Pratt's help. Paramedic Tony Gates returns and offers emotional support to a still grieving Neela, and it is revealed that he is becoming a new intern at the hospital. At the end of the episode, Abby (for the first time) invites her mother to visit them again as she tends to her infant son.

Pratt's excitement at becoming an attending is cut short when he has to teach the new interns and supervise the residents. Gates and Pratt argue over Gates' failure to keep his charts current and the treatment of a gay heart patient, which results in the patient's partner (John Mahoney) fighting his family over keeping him alive. Gates goes against Pratt's orders and saves the patient's life, but he is brain dead, which ultimately makes things worse on all fronts, especially with Pratt. After finding out Alex has not been talking to the psychologist that Sam set him up with, she confronts him and finds that Alex witnessed the shooting. Gates has sex with what appears to be his roommate. After visiting Abby and baby Joe, Neela meets the new chief resident of surgery, Dr. Dustin Crenshaw, who has a personality (and hair) that are very similar to the late Dr. Romano.

Abby enrolls in a "Mommy and Me" class and meets a group of nannies, which changes her outlook on childcare. A grandfather and grandson are injured in a chainsaw accident, leaving Kovač stuck upstairs with a difficult case. Pratt has his trial-by-fire when he has to handle the ER alone, juggling multiple traumas, teaching duties, and Gates, whose paramedic experience lead him to try difficult procedures unsupervised and dictate his notes, both of which infuriate Pratt. Neela mentors a new med student assigned to surgery and lends a hand when Pratt makes a serious error, to the scorn of the chief surgical resident. Sam discovers Alex's latest extracurricular activity. Gates turns out to be living with a woman, Meg, and her daughter, Sarah.

Curtis Ames (Forest Whitaker), a carpenter who had a stroke while under Kovač's care for pneumonia, sues him for malpractice. During the trial, each man's recollections of Ames' treatment are recounted via testimony and flashbacks. Kovač worries about the implications of the suit and the possible outcomes. Abby returns to work and must adjust to the dramatic changes in her life. An equipment shortage hampers Pratt, Abby, and Neela's treatment of a patient, leading them to attempt a risky procedure. Pratt's early morning trip to the barbershop results in a new awareness of community need.

A collision between a motorcycle and a car brings critical patients to the ER. Kovač and Ray treat the motorcycle rider, and discover a condition his wife wants kept secret. Abby and Neela work on the driver of the car, but his surgery does not go well and his wife soon has troubles of her own. Pratt has a new lady in his life, and a new roommate. Gates has a different kind of girl trouble, and we learn that Meg and Sarah were the family of Gates' friend Keith, who was killed during the Gulf War. Kovač gets some important news, and an unexpected visitor.

Ames is pursuing a hopeless quest to get an appeal hearing in his case. Hope goes behind Weaver's back to get free meds for a patient. Crenshaw and Lockhart get combative during an M&M session. When a combative patient returns later to the ER, he is a completely different person and has no memory of his earlier visit, and Morris has a good idea of what's going on but can't get anyone to believe him until Sam steps in to help. Kerry turns down an offer to be a TV medical reporter. Abby and Luka change their minds about hiring a nanny.

Three homeless kids come to the ER, one of whom presents with rabies and the doctors try extreme treatment to try to save him. An alcoholic is brought in unconscious after a bar fight the night before, hypoglycemic from lack of eating; his wife's injuries concern Kovač. Pratt and Gates have a confrontation over Gates' neglect of Pratt's orders. Tony explains his living situation to Neela. Greg finds Chaz and his boyfriend together and evicts Chaz from his apartment. Kerry is becoming dissatisfied with her reporter job. Greg ransacks the meds room for free samples to distribute at the church clinic.

It is Thanksgiving in the ER and Abby is called in for a transport by helicopter. The patient is unstable and ends up dying. Abby and the others in the helicopter then take over a new commission, a big car accident. She struggles to keep a little boy's mom alive who is stuck in a crashed bus. Meanwhile in the ER, Sam's son Alex is volunteering and keeps a patient, Lulu, company because her parents do not show up. Pratt turns to Kerry for advice on dealing with Chaz's sexuality. Neela decides to take things slow with Gates, yet she starts to make out with him.

A teenage girl is found in front of her school, bleeding and apparently raped. As Kovač and Gates treat her, Abby and Neela try figure out the truth about what happened, while Kovač must help the girl's mother, a colleague. When the police are no help with Ames, Kovač decides to confront the problem. Abby's friend from Ike's returns. Pratt struggles to cope when his brother fully comes out. There is a new nurse on the floor, but can he handle the ER? Meanwhile, Ray's got a secret and Gates pours on the charm, but Neela's not impressed.

It is Christmas in the ER. Kovač and Abby, as Rudolph and his elf, visit pediatrics, while Morris learns the meaning of Christmas when he plays Santa to a special girl. Ames takes action that creates tension between Kovač and Abby, leading Kovač to make a heartfelt confession. Teller returns, sending Gates and Ray on a mission, while Neela oversees an unusual kidney transplant case. Sam and Ben take a stand when a patient is dumped in an alley by Mercy Hospital. Morris gets an offer from Hope he can't refuse, but somehow does.

Budget cuts force Kovač to make a difficult personnel decision. As word gets around the ER, emotions run high. Abby wonders if Kovač is keeping a secret. Pratt's efforts at community service lead to an unanticipated turn of events. Gates' home life intrudes on the ER, affecting Neela. Morris' missing credit card has Sam concerned. A patient Kerry is treating relates the horrifying story of her family's destruction in New Orleans during Hurricane Katrina.

Dr. Pratt differs with Rev. Watkins over the church clinic and faces a hearing before the board. Lockhart's concern for Eddie causes tension between her and Kovač on the job. Barnett bickers with Gates and Neela over the treatment of one of two boys injured in a snowmobiling accident; the father assumes it was the stepson's fault and the stepson doesn't tell him the real story, leading Ray to tell the stepfather the truth about what happened and also upbraid him for being worthless. Tony still hasn't told Sarah he's moving out. Alex falls deeper into sullen rebellion. Kerry says her goodbyes. Abby finds out who Eddie really is but her follow-up on that is cut short due to another crisis.

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NOTE: Final regular appearance of Dr. Kerry Weaver.

Curtis Ames has broken into their apartment and threatens Abby and baby Joe with a gun, demanding that she call Kovač immediately. Once Luka arrives home, Ames takes him away at gunpoint and Abby immediately calls 911. Pratt has been arrested for his involvement in the church's medical clinic. Gates and Rasgotra respond to Sarah's call for help and find Meg unconscious with an unknown overdose. Alex accidentally sets the apartment on fire. In a moment of awareness, Meg tells Tony that he's Sarah's father before she dies.

The Medical Board suspends Pratt's license. Hope tries to own up to her involvement in the clinic, but Archie dissuades her. Rev. Watkins insists on accompanying Pratt to his board hearing. An aspiring stand-up comedian is desperate to get out of the ER for an important gig. Dubenko explains the new "exchange pool" for kidney transplants to Dr. Rasgotra, who is part of the surgical team. Sam's concern over Alex's worsening attitude problem grows. Things get more awkward between Neela and Tony.

Sam is overworked because some nurses are sick, others on vacation, etc. Gates and Kovač treat Anna Hayes (guest star Sean Young) who is vomiting and has an altered mental status. Sam is angry when a cop drops Alex at the ER after he stole quarters from a laundromat. Neela finds out unethical business is going on with the transplant program and blows the whistle on it. Ray takes action when he finds out the true story of how a shy cheerleader got seriously injured.

Sam is not in a good mood because of Alex. She is thinking of sending him away at a school for at-risk teens. Kovač, Morris, and Sam treat Mario Dustin, a 42-year-old ex-con who has been shot in the chest, along with Donnie, another injured man, and Mario's son Junior. Ray treats a man with a broken nose. Abby and Pratt work on the family that was trapped in a blizzard. Gates got a call that his drunk father is on a bender and was involved in a bar fight.

Kovač, Abby, Pratt, Morris, and the team treat the survivors of collision between a big-rig and family car, including the wife of the truck driver and the son of the car's driver. They suspect the truck driver was drunk but the real story is less criminal and even more tragic. Sam celebrates her birthday in the ER as she cares for a terminally ill photographer (Annabella Sciorra) who changes her outlook on life. Neela and Ray share some subtle signals. Gates is shadowed by a medical student who notices his errors. Wedding plans continue as Luka and Abby try to decide where to be married, but someone else is handling the bachelor party.

While taking a self defense class, Sam hurts the teacher's knee. Kovač and Gates treat a patient whose father has Alzheimer's disease and can't remember the death of his son, which bring memories back to Kovač. Meanwhile, Abby becomes slightly paranoid about Joe's health when he catches a virus. Pratt tries to reconnect with his brother and tries to fix things, learning that Chaz is looking at a potential career in the paramedic department- which leads Pratt to ask Gates for advice. Gates and Sarah find out the truth about Gates' paternity test.

A photographer named Diana goes back to the ER and notifies Sam that her cancer is spreading. Kovač needs to relocate all the staff to different departments of the hospital since the ER is forced to close. Chaz develops alcohol poisoning after he gets initiated by his EMT coworkers. Gates' father takes Sarah out to watch a movie and when they come back, Gates realizes that his dad has been drinking, which prompts Gates to pack his father's things and ask him to leave; they later get into a fistfight. Also, Kovač decides that he only wants to be a doctor and resigns as ER Chief.

The ER is closed for renovations and repairs. It's the night of the ER banquet, and Tony unexpectedly shows up to go with Neela. Luka reveals to Abby his secret agenda for the evening: a surprise wedding; Abby is less than thrilled at both the idea, and that Hope helped Luka plan the whole thing, but is finally persuaded. One last glitch - the Justice of the Peace can't make it and sends a replacement, a rabbi! Tensions between Tony and Ray over Neela reach a breaking point.

Since Luka and Abby are unable to use the honeymoon suite reserved for them (childcare issues) Archie and Hope take advantage of the opportunity to further their relationship. The ER is open once again and wait times are just as bad as ever, which Dr. Moretti, chief of the ICU and assigned to evaluate ER performance, finds unacceptable. Dubenko is conducting an internal audit of the post-op unit due to increased morbidity and mortality. Ray is MIA. A lawyer gives Tony reassurance he will be able to keep custody of Sarah.

Luka leaves for Croatia to visit his ailing father. Ray is still MIA. Moretti has accepted the job of ER Chief and spends his first day auditing procedures. Gates loses his bid to get custody of Sarah (her grandparents arrive with legal documents demanding custody); he is left to assure a tearful Sarah that he will see her as often as he can. A drug-addicted Iraq War veteran turns out to have been an interpreter at torture sessions. Neela finally receives a call from a missing Ray's cell phone. She goes to see him in a hospital, only to find that he has had both of his legs amputated due to his accident.

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NOTE: Final regular appearance of Dr. Ray Barnett.