The cops and everyone else in the ER are attacked by multiple gunmen with machine guns. Faith is horrified when Bosco is shot multiple times. A huge battle ensues in the ER, and the cops eventually win. Ty and Sasha are both injured while battling one of the gunmen, but they manage to save eachother's lives. Kim realizes she can't be a paramedic anymore, and after telling Jimmy that she's pregnant, she accepts his marriage proposal and decides to quit her job. Dr. Field tells Grace that the surgeon that worked on Bosco's mom complimented him on a perfect tracheotomy, and he warns her not to be so rash again, but they part as friends, particularly since Grace helped save his life during the shoot-out. Faith has to tell Bosco's mom, who is recovering from her accident, that Bosco is in surgery with multiple gunshot wounds. Cruz figures out that Yoshi is working for Mann, and gets Yoshi to take her to Mann's apartment. Faith follows them, and as Cruz is trying to actually arrest Mann, Faith shoots him in cold blood.

Cruz convinces Faith to say that Mann was going to stab Cruz, and so Faith shot him to save Cruz's life. Faith is angry to be indebted to Cruz, and her day just gets worse when Fred files for divorce and says that he wants full custody of her kids. When Faith gets a meritorious promotion to detective, her first instinct is to turn it down, but Sully tries to convince her that this is an opportunity she shouldn't pass up, and it will only help her get custody of her children. Finney, a ranking internal affairs officer, is out to get Cruz, convinced that her story with Faith is only to cover up Cruz's misdeed. Cruz meets her new boss, Lt. Miller, who tells her that he's here to get her under control, and immediately demonstrates how effective he is going to be. Cruz gets a mysterious phone call telling here there's an IAB rat in her precinct, and she thinks it must be Miller. Ty and Sasha start a romance, and Sasha tries not to let it affect them at work when they're partnered up. Ty and Sasha arrest some girls in a stolen car and later find out that the girls are murderers. When Ty concocts a necessary lie about why the girls were originally arrested, Sasha refuses to support him even to keep a murderer behind bars. Sasha meets with Finney and tells him about Cruz's mysterious tip. Finney tells Detective Monroe that she's safe since Cruz thinks the rat is Miller. Finney says he know something was wrong with that shooting, because Mann had handcuff marks on his wrists, and he encourages Sasha to prove that Cruz shot Mann in cold blood. Bosco will live, but will be lucky if he can even feed himself when he recovers. Even though Faith knows this, she clings to the idea of being his partner again when he recovers.

Ty is saddled with a brash rookie cop named Brendan Finney, who is not only the son of the IA officer Finney, but is also a cocky wise-ass. Sully and Finney almost come to blows, partly because of Finney's mouth and partly because Sully hates his father. Finney quickly learns a lesson on the street when he has to write down the last will and testament of a doctor who was in a car crash and knows that she's going to die. Monroe hates that she's trying to entrap Cruz, but she does her job and buddies up to a lonely and promoted Faith to get the inside scoop on Mann's shooting. Cruz is kept on a short leash by Miller, but he gains a little respect for the sergeant when she quietly solves a gang shooting in Chinatown. Carlos, who is still futilely hitting on Grace, believes he's been cursed by a crazy psychic. Holly not only uncurses him, but gives him a big passionate kiss as well.

Faith visits Emily at school and Emily asks after Bosco, but isn't very comforting to her mother. Finney Sr. puts more pressure on Sasha to get Faith to give up Cruz, threatening her with exposure if she doesn't produce evidence soon. Finney Jr. tells Ty that their fathers both used to work with Sully, and Ty tries to get Sully to talk about the past and explain why he hates Finney Sr. so much, but Sully tells Ty to stay out of it. Responding to a domestic disturbance call, Sully and Sasha discover a three-day-old stinky suicide, and Sully sticks Finney Jr. with baby-sitting the corpse. Faith, partnered up with Jelly on her first day as detective, investigates the suicide, which Jelly decides is pretty cut and dry. Faith takes the extra time to view video-tapes from the victim's apartment, and discovers that a red-headed woman named Cindy is in danger from a mail-bomb. Faith manages to save Cindy, and the school children she teaches, from the bomb. Grace teases Carlos about his "girlfriend," Holly, and has her own eye on Finney Jr. Sasha and Ty make peace and decide to give their romantic relationship a try again, but then they discover a woman's body on it with a note around her neck: "Lieutenant Miller, I'm not going away."

Faith is put in charge of the body that Sasha found, and Lt. Miller assists in the investigation. Apparently, the young woman, who has been completely drained of her blood, is part of a serial killer case that Lt. Miller was working on in Brooklyn homicide before he stepped on his boss's toes and got transferred. Cruz realizes that Lt. Miller couldn't be the IAB rat after all. Miller and Faith, after some initial head-butting, work well together, but still find the case hard to crack. After they make an incorrect arrest, the real killer kidnaps one more girl and turns himself in, leaving her to bleed out unless Lt. Miller can find her first. Carlos tries to talk to Holly about how they're not a couple, but she sleeps with him and further muddies the issue. Grace and Brandon Finney meet in a bar and have a passionate tryst. The next day, Carlos and Grace respond to a fake call that turns out to be an ambush by two guys with a gun who want their drugs. Carlos gets knocked out trying to protect Grace. Ty and Brandon show up because Brandon wants to see Grace, and Brandon ends up shooting the druggie that has a gun to Grace's head. Grace is grateful, but Brandon can't really talk about it.

Faith and Miller race against time to find the young girl before she runs out of blood. Barton, the kidnapper, says that they are the greatest detectives in the world, and so they should be able to stop him, but he won't tell them where she is until they run out of time at 6am. Miller finds Barton's apartment, but all that's there is the refrigerated blood of the other girls he's killed. Finally, at 6am, Barton tells them where they can find the girl's body. Luckily, Faith and Miller lied to Barton about the time, so they find the girl just barely alive. Brendan Finney doesn't think he needs counseling after the shooting, and his father agrees, praising his boy for being a fabulous cop so soon after joining the force. Grace is still freaked out from the experience herself, but pushes Finney away when he tries to talk to her. Carlos is admitted overnight for observation and given a CT 'cause he's been getting hit in the head so much lately, and Holly swears she won't leave his side. Ty and Sasha reunite in bed, and Ty finds a picture that Sasha had of the knife that was found in the pool with Mann's body. He mentions that he thinks it's weird that Sasha would keep a picture of the knife that was almost used to kill them, and says that he didn't even realize there was a picture of it... the last time he saw it Cruz had it. In front of both Brendan and Faith, Cruz is arrested by the elder Finney for the murder of Donald Mann.

Cruz is arrested, and quickly assaulted in lock-up. At her hearing, the judge doesn't grant her bail and puts her in Riker's until her trial date. To save her life, Cruz starts a fight at Riker's in front of a guard and gets put into isolation. Faith is in the middle of a custody hearing with her husband and her kids when IAB officers come and take her away. She is furious and scared, but C.T. Finney assures her that once she gives a statement against Cruz, she can go back to her hearing. Faith craftily gets herself full immunity in the Donald Mann case before giving her true statement that she was the one who shot Mann. Finney is furious with Monroe, who says she warned him they weren't ready to arrest Cruz. Cruz is set free. Faith tells Cruz she still doesn't like her and didn't want her help, so she doesn't owe her anything. Cruz says it doesn't matter, she doesn't rat out cops no matter what. Holly is disappointed with the way that Carlos deals with an obviously suicidal and slightly disturbed woman. When the woman finally stands on the ledge of her building, Sully tries to talk her down, while Finney makes the brash move of climbing out to save her. Both cops fumble the job, and the new firefighter, Stu Szczelaszcyak, rescues the woman with a ladder. Sully yells at Finney, calling his dad a liar and a murderer. Ty later asks Sully what that was all about, and Sully admits that he believes C.T. Finney was responsible for Ty's father's death. Rose is by her son's bedside when Bosco finally opens his eyes.

A Councilman, Daniels, is attacked and raped, but even when she catches the perpetrator, Cruz can't get Daniels to file a complaint. Instead, Daniels goes off the deep end and goes after his rapist with a gun, and Cruz ends up using the story of her own rape to talk him out of killing himself. Ty tells Monroe about Sully's suspicions about C.T. Finney being responsible for his father's death, and Monroe goes digging. Ty talks to the man who killed his father, Raymond Morris, who tells him that C.T. Finney got him to do it, and he tried to tell Sully, but Sully didn't do anything. Ty confronts Sully, and Sully admits that he thought it was better not to rock the boat and let Ty's mother have his dad's pension. Monroe interviews Brian McKinley, whose name she found in Ty Senior's file. McKinley gives her proof of the coverup, but warns her that she might not want to use it. In jail, another prisoner murders Raymond Morris while a guard watches. Faith finally meets her husband's mistress, Caroline, face-to-face when her son, Charlie, goes missing. Faith and Caroline search for Charlie together, but later Faith finds Charlie outside the door of her apartment. Cruz tries to figure out who told IAB about the knife the she placed at the scene of Donald Mann's murder.

Sasha leaves the incriminating documents that she got from McKinley at Ty's door. Ty talks to the chief of police, who tells Ty that he'll help him, but then secretly calls C.T. Finney. C.T. Finney invites both Ty and Sasha to his office, and exposes a miserable Sasha to her lover. C.T. Finney tells Ty that he knows about the falsified ticket (from "Alone Again, Naturally") and threatens to push it as a felony if Ty continues to pursue his vendetta. A disappointed but determined Ty leaves C.T. Finney's office, with Sasha running after him begging to let him explain herself. Ty tells Sasha not to ever talk to him again. On Carlos's advice, Finney apologize to Grace for being insensitive, and they agree to give their relationship another try, but this time take it slowly. With Ty pursuing his personal matters, and Sasha being called away to IAB, Finney ends up partnered with Sully. Sully realizes that Finney has no idea who is father really is, and subtely decides to give the rookie a chance to prove himself as his own man. Faith and Jelly investigate the murder of a Muslim girl. When Faith finds out the girl was dating a boy behind her father's back, and was 8 weeks pregnant, she thinks the girl was killed by her own father as an honor-killing. However, after they get the girl's boyfriend's cell phone records, they realize that he was the one that killed her. When they go to his house to pick him up, he drives away, and suicidally drives into the river. Finney performs another thoughtless but heroic move by diving in after the car and rescuing the boy. Faith tells Bosco about her marital problems and the custody fight over her kids. Faith tells Bosco how much she's missed having him to talk to. Faith is amazed when Emily comes to her apartment and tells her that she told the judge she wanted to live with her mom.

Amazingly, Sasha is not reassigned by C.T. Finney, who has apparently left her out to dry, so when she shows up for morning roll, Ty outs her as IAB to the entire squad. Cruz and Faith both have it out with Sasha personally, and the rest of the squad ignores and scorns her. She also finds a dead rat hanging in front of her locker. Cruz picks up a case in which an eight-year-old girl was shot by a drug dealer named Skeeter, and she tells the squad to keep an eye out for him. Sasha, along with Finney, who is the only cop that will partner up with her, find Skeeter. They call for backup, but no one responds. In the ensuing fight, Sasha loses her gun and gets beat up pretty badly. Finally Ty and Sully respond, and show up just in time to see Sasha almost shoot Skeeter in cold blood. Ty realizes what a mess he's into when he finds out that both Raymond Morris, his father's murderer, and Brian McKinley, the ex-IAB officer that gave Sasha the incriminating file, have been murdered. Sully offers to testify on Ty's behalf, but Ty fights him on it, not wanting to get Sully into more of a mess than he's already in. New firefighter Stu finds himself playing host to his favorite old action star, Carter Savage, who is researching the FDNY for an upcoming movie role. Stu is sadened to find that Savage is now nothing more than a moody and desperate alcoholic.

Sully reluctantly works with Monroe, since they both want to help Ty and bring his father's murderer, C.T. Finney, to justice. Monroe looks up more of Sully's old anti-crime unit from back in the day, and they travel all over the place gathering up these sad old men to testify against Finney. They bring all the men to the DA's office, along with Ty, who is blown away. The DA bring Finney in and shows him that everyone is prepared to testify against him, and that he should turn himself in. Monroe hopes this will help patch things up with Ty, but Ty says he's grateful, but still doesn't really want to talk to her. Ty goes and finds Brendan Finney to tell him about what's going on with his dad.

Brendan helps out a young scared kid who sprains his wrist while in the playground with his baby sitter. C.T. Finney, instead of turning himself in, calls Brendan to tell him that he loves him, and committs suicide in his running car in the garage. Brendan and Ty find him, and Ty helps Brendan make it look like an accident to make sure his mother can still get her husband's pension. Carlos can't tell Holly that he loves her when she tells him that she loves him, but when Holly is peripherally involved in an explosion at a coffee shop, Carlos realizes how much he really cares for her. Cruz investigates one of the men injured at the exploding coffee shop, and finds out that he has stolen someone else's identity. Cruz unwillingly works with a federal investigator, Rice, who is on a terrorism task force, when it turns out that the guy she is investigating is a terrorist. Cruz and Rice capture another related terrorist, and realize while they're trying to interrogate him that he is suffering from severe radiation burns. Faith visits a slowly recovering Bosco in the hospital.

Grace and Carlos respond to the call for paramedics to the 55th precinct police station, and they realize that the terrorist still has the radiation source on him, taped around his mid-section. The precinct house is temporarily evactuated, and Cruz, Rice, Carlos and Grace all go to the hospital to get checked out, along with the terrorist who dies en route. Their tests all come out okay, but Dr. Fields finds out that there is something else very wrong with Cruz that she's not dealing with. Cruz finds the terrorist's car and uses it to track down the guy behind the plan, who she takes down just after Rice is shot in the leg. Brendan attends his father's wake with his family. Ty stops by, as does Grace, who offers Brendan some unique comfort during this difficult time. Sully enrages Ty when he scoffs at the whole story of C.T. dying while working on his car right before he was supposed to turn himself in. Through a misunderstanding, Carlos drives Holly even further away, and when he goes to her apartment to apologize, all he finds is a note saying that she's gone home. Faith and her daughter have a mellow night at home together. Bosco is released from the hospital and is greeted with honor by most of his precinct outside the hospital doors.

Monroe is pregnant, and continues to work with the squad, even though no one wants anything to do with her. She tries to talk to Ty, but he doesn't want to talk to her. The kid who fell in the playground (that Brendan befriended two episodes ago) calls Brendan's cell phone. The kid, Ben Reynolds, tells Brendan that his daddy is hurting his mommy, and when Brendan finally arrives at Ben's apartment, he finds his mother stabbed and Ben missing. Brendan and Ty work with detectives Faith and Jelly to track down Ben and his father, who has gone off his psychotic medication. They finally track them to the printing house where Ben's dad used to work, and they end up in a car chase. Ben's dad, cornered, threatens to slit Ben's throat, but instead lets his son go and slits his own throat. Brendan counsels a confused Ben on loving his father even if his father has done bad things. Carlos is in a foul mood since Holly left, and Grace tells him to stop bitching at her. Grace says she'd rather deal with blood and guts than love anyday. Brendan finds Grace at the firehouse and says he'd like to be more serious with her... perhaps really boyfriend and girlfriend. Carlos is jealous of the happy couples on the street.

Bosco is allowed back on the force once he requalifies, but his vision is fuzzy in his right eye and he can't shoot straight. He asks Faith to shoot for him, but she points out that he shouldn't be back on the streets if he can't shoot. Bosco gets bent out of shape and thinks that Faith is letting him down; he insists that he can't sit behind a desk for the rest of his life. Cruz is told by her doctor that if she doesn't get treatment, it's a death sentence, but Cruz says she'd rather enjoy her life than prolong it. In pursuit of a gangbanger, Maddox, who has been burying bodies of murder victims in other people's coffins, Cruz is more reckless than ever, and Santiago worries about her. Carlos tries to report Holly missing, but no one will take him seriously because she's still officially on vacation from work. Grace runs into a heroin-addicted homeless woman who turns out to be her mother, a nurse who became addicted to morphine while serving in Vietnam. Grace wants to take her mother to dinner that night and talk to her, but her mother runs away. Monroe is forced to admit to her partner, Sully, that she's pregnant, but makes him promise not to tell Ty. Sully tries to encourage Ty to talk to Monroe, but he's not interested.

Crossover with Medical Investigation

Two guys rob a jewelry store and kill the proprietor. The guy who fired the lethal shot gets away, but his partner, who is AWOL from the Army and was recently stationed overseas, is caught and hospitalized with a strange illness. Dr. Hickman is so worried, she calls in Drs. Connor and Durant from the NIH, who identify the patient as having a rare and dangerous viral infection. There is another patient at Beth Israel who has it, and Carlos, who has just had a happy reunion with Holly, has been exposed and collapses with a high fever after vomiting. Sully continues to encourage Monroe to tell Ty about her pregnancy, but she wants a chance to work things out on her own with Ty before telling him about the baby. As Cruz and Santiago take Maddox to central booking, he is shot in the police station by a young boy. When a man named Marcel Hollis arrives with a lawyer to take care of the boy, Cruz finds out that Hollis was Maddox's second in charge, and is now taking over the 108 (Maddox's gang). Cruz can't find a away to arrest Hollis, so he remains free to brutaly get rid of his competition. Faith finds out that Bosco requalified, but he blows her off when she asks him how. Faith decides to do a little investigating.

Carlos and the gang behind the jewelry store robbery are hospitalized with what the NIH doctors figure out is a strain of Marburger's disease, a rare disease that causes its victims to bleed to death. Holly holds a vigil by Carlos's bedside (or, as close as the doctors will let her get) while the other patients around him slowly bleed to death. The doctors collect more people who are dying or have already died from the disease. They are distracted by a red herring when they find out that a vial of Marburger is missing from a nearby lab in New Jersey, but it turns out that it isn't the source of the infection. Faith and Dr. Connor work together to figure out that the members of the jewelry heist gang are also smugglers, and when they find the smugglers' boat, they find an African monkey who has died from Marburger - the source. Carlos makes a miraculous discover and has another happy reunion with Holly, who never got infected herself.

While the cops are identifying the remains of the four gangleaders that Hollis blew up, Hollis rallies the rest of the gangleaders together into a kind of board of directors, promising them that their "soldiers" will far out-number the cops. Cruz immediately knows to go after Hollis, but is surprised when he comes to her. He tells her that things are going well, that there's no war in the wake of Maddox's death. She wants to get him for the four murders, but he has a perfect alibi. When Cruz hears that the young boy who killed Maddox, Michael, is being charged as an adult, she goes to talk to his mother, Deborah Dawkins. Deborah admits to Cruz that Hollis gave Michael the gun he used to kill Maddox, and Cruz arrests Hollis. Hollis warns Cruz that she's making a mistake, that innocent people will die if he's locked up. Cruz is horrified when, late that night, there is a drive-by shooting at a bus stop and six people are killed, including a nine-year-old girl. Bosco is back on the force and paired with Sully. Bosco is a little defensive about his recovery, and Sully is a little defensive when Bosco starts talking about Sasha, but otherwise, they get along okay, and Sully actually ends up telling Bosco how much he admires that Bosco never lets the system get him down. Bosco and Sully discover a woman lying in a pool of blood on her kitchen floor, and find out that her vampire-loving 15-year-old daughter is missing. Faith gets the case, and works it with Bosco and Sully, visiting the vampire club downtown where the daughter hangs out. Faith pisses off the head vampire there, Dante, hoping he'll lead her to the daughter. Faith finally finds the daughter at a friend's house, where the girl admits to trying to kill her own mother. Meanwhile, the pissed-off head vampire, Dante, decides to approach Emily Yokas, Faith's daughter, and pretends that he met her at a friend's party. Sully worries that Ty is starting to date someone else and still hasn't talked to Sasha. Holly comes back to work earlier than expected because she realizes that Carlos is no fun to be around when he's sick.

Ty and Brendan pick up one of two robbers, and Cruz sends them undercover as construction workers to get the second. Ty goes to a hot dog truck to get Brendan and himself some lunch, and ends up getting a little something extra from the sexy woman who runs the hot dog truck. Brendan later notices that the woman is running a prostitution racket out of her truck, and Ty is horrified. Brendan and and Ty chase down the second robber, and Brendan tells Cruz about the hot dog lady. Ty shushes him, but it's too late, and Cruz arrests the hot dog lady, who not only knows Ty, but a lot of other guys on the job. Bosco is so desperate to be back on the streets that he volunteers to partner up with Sasha. While he doesn't approve of what she did with IAB, he doesn't necessarily hold it against her either. Sasha finally decides to be excited about her pregnancy, but hasn't quite yet told her sergeant or her coworkers. While Sasha and Bosco are dealing with a disturbed woman who can't get her welfare check and has decided to hold the welfare office manager at gunpoint, Sasha gets into a struggle with the woman and Bosco accidentally shoots his partner. Sasha goes into surgery and loses the baby, although she'll be okay. Sasha's sister thinks Sasha was shot on purpose, but Sasha knows that's not true. Ty finds out that he just lost a baby he didn't even know he had, and goes to Sasha's bed side. Faith tells Bosco she's worried about him being on the streets, but Bosco doesn't want to talk to her about it. Cruz realizes her illness isn't just going to go away on its own when her gums start spontaneously bleeding at work. She sees her doctor, who tells her that her only recourse at this point is chemo, because her immune system is shutting down. Manny notices Cruz's pamphlet on chemo, and tells her she's not as alone as she thinks she is. Faith realizes Emily is lying to her and dating a guy named David.

Fearing death, a distracted Cruz delves into the frightening world of the cultic Santeria after a woman is burned to death and encounters a mysterious practitioner (Reg E. Cathey) who knows her condition -- and soon, even Cruz softens when she thinks she sees her dead sister. Elsewhere, Carlos is upset when girlfriend Levine takes him to meet her backwoods parents in Virginia where he learns a bit too much about her family. Meanwhile, Faith urges Bosco to admit his vision is too impaired to stay on the streets. Ty and Sasha reconcile their problems.

Ty and Brendan are injured and two parents are murdered in a bizarre traffic tie-up that climaxes when a driver goes berserk and shoots the victims while allowing their teenaged son (as Stephen, Peter Scanavino) to escape. But Faith discovers another slaying - all of which are all connected to a cult that thrives on kiddie porn and child abuse. Cruz looks to break up a lethal gang war while pondering her recent experience with the Santeria sect. Emily Yokas is persuaded by the vampire-worshipping Dante (Luke Robertson) to come to his lair that night. Carlos wants to buy an engagement ring.

Faith tries to negotiate a peaceful ending to a televised hostage crisis where a young man Tommy (Chris Stack) threatens to kill his father who sexually abused children while heading a bizarre religious cult. All the while, unbeknownst to Yokas, her own daughter Emily is being held captive at home by a wannabe vampire Dante (Luke Robertson). Cruz vows revenge when her partner Santiago (Manny Perez) is shot as payback in a deadly gang turf war. Carlos is frustrated in his attempts to propose to Levine, and Grace agonizes over a comatose Finney.

Third Watch goes out in a blaze of glory when gangbangers assault the 55th Precinct station and set it afire, trapping Cruz and Monroe. While Bosco and other police return fire, the future of their beloved "Camelot" house is in dire jeoparady -- as is the life of one dedicated cop. In the confusion, murderous gang leader Marcel (Wyclef Jean) escapes, Faith fears for her visiting daughter's safety -- and a nervous Carlos preps to propose to Holly. In the final minutes, fans will also learn what the future holds for their first-responder heroes. Former cast regulars Michael Beach, Eddie Cibrian and Kim Raver join recurring star Aidan Quinn as guest stars. Coby Bell, Cara Buono, Josh Stewart and Skipp Sudduth also star.