The shoot-out ends with Bosco shooting Noble, Faith shooting Cruz, and Cruz shooting Faith back. Noble dies, Cruz is only mildly injured, Faith has a bullet lodged near her spine and is in surgery, and Bosco spills the whole story to the boss, Lt. Swersky, but lying to save Faith and saying that it was he who shot Cruz. Bosco tries to check on Faith, but an enraged Fred Yokas demands that Bosco stay away from his family. Surgery on Faith goes well, but the bullet is still by her spine and she hasn't woken up yet. A badly burned Lt. Johnson begs Jimmy and Doc to put him out of his misery, and finally Doc does so with Lt. Johnson's wife by his side. Kim is overwhelmed by mourning the deaths of Alex, Aaron Noble, and Lt. Johnson all at the same time, and Jimmy comforts her. Ty feels like he isn't worthy of mourning Alex's death since he wouldn't introduce her as his girlfriend to his mother. Bosco finds out that Noble was actually working for the FBI, and Cruz was his FBI handler.

On his last day on the street as a paramedic, Doc tries desperately to place blame for Alex's death. He tries blaming himself and even blaming Alex, but he holds a grudge against the trainee that didn't show up forcing Alex to work a paramedic shift. Doc goes so far as to visit the trainee, Eugene Rossi, at home and violently chastise him. Alex's mother asks Doc to speak at the funeral, but Doc can't even bring himself to attend, so Carlos comes through. Carlos says that someday he wants to be as brave as Alex was, and tells Mrs. Taylor how Alex said to be sure to tell her that it didn't hurt. Kim supervises the new paramedic, Eugene, but is more distracted by the fact that she had unprotected sex with a now dead intravenous drug-user. Jimmy tells Kim he'll accompany her to the doctor to get tested. Bosco, who finds himself increasingly unpopular at his own police house, tries desperately to save Faith after the FBI leaves her out to dry. Bosco threatens Cruz with revealing all her past legal indiscretions if she doesn't tell the boss that Faith shot her accidentally. Cruz finally changes her story at Bosco's request, and Bosco tells Faith she's off the hook, but Faith doesn't really care so much since she's a bit distracted by waking up and finding herself paralyzed.

Things are starting to get back to normal around the 55. Kim gets tested for sexually transmitted diseases, and when she finally gets the guts up to look at the results, she's pleasantly surprised. Doc, to no one's surprise, has trouble adjusting to working in an office, and takes the first opportunity he can find to get back out on the street. Doc tells Carlos that the new guy, Eugene, probably won't make it as a paramedic. Carlos is partnered with another new paramedic, a strange but competent woman named Levine. Bosco, partnered with Sasha Monroe, insists on staying outside Faith's apartment in case she needs anything. Faith, finally back at home, has trouble adjusting to being weak and needing care, and her overbearing mother-in-law coming by to lend a hand doesn't help. Sully and Ty chase down a truck that blows through the checkpoint at the Brooklyn Bridge, and find it filled with 40 illegal immigrants from China, some of whom are infected with The Plauge. The cops who aren't already quarantined at the hospital, including Sergeant Cruz who is now stuck back in uniform, chase down the one illegal alien that escaped, and are relieved to find out that he wasn't infected. Ty runs into an ex-girlfriend from law school, Sharon, who is now an ADA.

Jimmy becomes the new fire lieutenant in the wake of Johnson's death, but his men, particularly Billy Walsh, aren't ready to take orders from him yet. Kim, a new supervisor herself, counsels Jimmy on how to deal, and the two, almost out of habit, end up sharing a romantic kiss. Jimmy finally makes peace with both Walsh and his own leadership. Faith seems to have given up hope, and resists the efforts of her physical therapist to start rehabilitation. Faith's mother, who has been around helping out the family, does a masterful job of manipulating Faith back into fighting for herself. Monroe and Bosco, who are adjusting to being partners, deal with a rap artist who is sending his minions around town to destroy bootleg CD operations. Ty reconnects with his old girlfriend, Sharon, who urges him to get back into law school. Sully challenges Ty that if they take the LSATs together, Sully will score higher.

Doc, who is acting weirder and weirder, bonds with Kim over their "gift" of being paramedics, and then officially reprimands her for administering medication in the field without prior authorization. Sully saves a prominent judge's life when a car bomb goes off, and then is assigned to the special detail to protect her. Sully and Ty have to hunt down the judge, Judge Halsted, when she sneaks out to get coffee, and then Sully watches helplessly as a flower bomb goes off in the judge's house, killing the judge's housekeeper and injuring Ty. Faith's doctor recommends she see a psychiatrist for the severe pain she's getting in her neck that they can find no medical cause for. Cruz convinces her lieutenant to let her work an undercover operation busting a prostitution business that's run out of a medical office. Cruz, working with Monroe, gets gung ho about busting the johns, but when one of the johns surprises her and rapes her, an observant Monroe has to convince her to go to the hospital for a rape kit instead of showering off the evidence.

Faith sees a psychiatrist, and finally gets some of her anger out about the fact that no one is being held accountable for her injuries. She also admits wanting to shoot "that bitch" Cruz. Cruz finds out that her rapist's name is Thomas Warner, and he makes a habit of raping prostitutes at the office she was working. She forces Monroe to wait with her to bust Warner coming back to the office, and almost misses testifying at the hearing for the trial of the drug-dealer, Animal, that killed her sister. After Judge Halsted's housekeeper dies, Sully brings the judge back to his apartment for safe-keeping, and they get to know each other a bit better. Judge Halsted is the judge on Animal's hearing, and the cops think it's Animal that's after her. After delivering the judge safely to her court room, despite a sniper outside the court house, Sully tracks a man that got a signal from Animal in the court room. Sully and Ty follow the man to a nearby house where he meets up with the flower-bomb delivery guy. Sully sneaks around back, and Ty confronts the men when they start loading the trunk of a car with large bags. The flower guy says he has a detonater, and can blow the whole city block away. Ty drops his gun, but Sully sneaks up and shoots the guy from behind.

With some expert marksmanship on Sully's part, he and Ty take down the bomber and intimidate a confession out of him. Judge Halsted confronts the bomber, but then shows a softer side when she asks Sully to have a cup of coffee with her after arriving at Sully's favorite diner on her motorcycle. Cruz is distraught when the prostitution ring she was working gets busted, and tries to make sure that Thomas Warner is arrested for rape. When she can't get a case to stick with the testimonies of two prostitutes, Cruz finally admits that she was raped too. Even though Bosco gives her the opportunity, Cruz doesn't harm a hair on Warner's head, but in lock-up, Warner quickly finds himself the target of two thugs who say that Cruz sent them. Carlos and Eugene, in their ambulance, are hit by a city bus when the driver has a heart attack. Doc arrives on the scene and completely overreacts to a situation with Eugene, going so far as to get into a physical altercation. Eugene decides to file charges against Doc, and tells Kim and Carlos about Doc's visit to his house. Carlos tries to talk to Doc about the situation, but quickly realizes that Doc is completely and irrationally convinced that Alex's death is all Eugene's fault. Faith, who is having flashbacks of being shot, realizes she's not the same person that she was before she became a cop, and asks Fred if they can leave town for awhile.

Doc gets demoted and is back at the 55, although he lies to everyone and says that he came back by choice. Doc and Kim immediately butt heads, and Doc is acting even more reckless and irrational. Cruz tries to get back to normal, but she still feels like she has something to prove. Cruz and Bosco are horrified when Animal makes a deal with the FBI to give up Buford. After the FBI bungle one attempt to bring in Buford and Animal is murdered in jail, Cruz and Bosco work together to undercut the FBI and get Buford themselves. In a nail-biting operation, they bring down Buford and Cruz manages to keep her rage in check and not kill him before arresting him. Carlos finds out that the daughter he gave up for adoption, Kylie, has aplastic anemia and needs a bone marrow transplant. Carlos is tested, but he isn't a match. Ty teases Sully about his relatioship with Judge Halsted while Sully continues to bug Ty about taking the LSATs.

When Carlos gets desperate to find a bone marrow match for his daughter, Kylie, Doc encourages him to dig into his own familial past. Carlos finds out that he wasn't abandoned by his parents, but was found clinging to his dead father's hand after a car accident. Doc gets Carlos air time on NY1 News, and in the barrage of resulting phone calls Carlos is amazed to hear from his mother. Carlos wires his mother money to fly to New York from Los Angeles, but she never shows up. Bosco and Monroe find themselves going after a small-time mobster/restaurateur, Allie Nardo, who is trying to squeeze out an honest family-run linen company. After the son of the linen company family dies in a suspicious fire, Bosco and Monroe come up with a plan to slap Nardo with so many small violations that he ends up in jail for awhile.

Kim and Jimmy spend a romantic Christmas together as a family. Doc gets more and more bitter as he spends Christmas alone. Sully saves a precocious 12-year-old girl from a fire and the feisty orphan convinces him to play Santa at her childrens' shelter. Monroe is desperate find an Oliver the Onion toy for her nephew, but every store is already sold out. After Bosco and Monroe arrest a Santa from a toy store who is a child molestor, the toy store owner gives Monroe an Oliver the Onion as a thank you, but she can't take the gift. Lt. Swersky feels bad and makes sure that the Onion finds its way into Monroe's locker anyway. Monroe and Bosco use their connection to the toy store owner to help a man whose Christmas presents for his five kids have all been stolen on Christmas Eve. A man turns up from Hawaii claiming to be Carlos's brother. After being burned by the "mother" incident, Carlos ignores him until he finds out that the man has already been tested and is a bone marrow match for Kylie.

Bosco and Sasha are called to a quiet neighborhood by an anonymous caller who says he heard a call for help from below his window. They discover a 21-year-old boy named Tommy with a bad cut on his hand and call an ambulance to check him out even though he says he'll be fine. Cruz happens across them and lends a hand. Kim arrives with a bad-tempered Doc and they bandage Tommy's hand. In the meantime, Bosco and Sasha discover a huge amount of blood on the side of a building. Bosco searches Tommy and discovers that the boy is carrying two knives. Doc is furious that Bosco didn't search the guy before, and becomes livid when Bosco handcuffs Tommy to Doc's bus. Ty and Sully arrive to help out, as does Carlos with a second bus. Sasha thinks she sees a body in a shed, and Bosco uses Tommy's keys to open it. A badly disfigured bloody body rolls out of the shed door. Bosco and Sasha take a handcuffed Tommy to the hospital. Tommy just keeps making up new lies. Cruz seems to be softening around the edges a bit, asking for Sully advice and thanking people for doing things.

At Kim's urging, Jimmy agrees to keep their burgeoning relationship a secret from both their son and the firehouse. Sully and Ty discover a woman in her car who has been raped, beaten and robbed, and runs in terror when she sees them. Sasha and Cruz discover a woman who has been beaten and robbed near her car. The woman is unconscious, but her young son, who is hiding nearby, runs in terror at the sight of them. The cops realize there are two men posing as cops and terrorizing the neighborhood. Once the news gets out, being a cop becomes dicey. Sully and Sasha have to chase an elderly woman down who drives dangerously just to get away from them. Bosco and Cruz find themselves questioning, and pissing off, other cops. Kim, driving her mother's car, is pulled over by two cops, and realizes something is amiss. She maces one of them and runs for it, screaming for help. Cruz and Bosco notice her pulled-over car and come to her rescue. In the ensuing gun fight, one of the fake cops tries one last time to trick the cops into thinking he is one of their own, but Bosco sees through him. Kim, safely back in Jimmy's arms, says she wants to tell everyone, including Joey, that they are back together. When Sasha considers taking the sergeant test, Cruz mentions that she was promoted meritoriously for actions in the field, and worries that she's not a good boss since she never took the test.

Jimmy proposes marriage to Kim, and Kim happily accepts. A new captain, Jack Steeper, show up at the firehouse with no warning, and Doc is sure that he's there to shut the place down. Steeper informs Jimmy that he's been promoted to the Bed-Stuy rescue squad, a move that Jimmy is happy about. Jimmy and the other firefighters get called out to a warehouse fire in which Jimmy almost dies. When Jimmy talks later about how he was ready to die, Kim realizes she can't be married to a firefighter again, always worrying that he'll die in the next fire. Kim gives Jimmy back the engagement ring. Even though Jimmmy is no longer working out of the 55, he tells Kim that he's not giving up on them. When a little girl is hit by a car in Harlem, a group of teens hunts down the driver and the driver ends up dead. Cruz arrests Tony, a known felon, and Tony confesses to the crime. Sasha is sure that she saw Tony across town just before the crime took place, and finds an elderly witness who saw a different boy, Lamont, hitting the victim. Tony finally admits to Sasha that he's taking the fall for Lamont because Lamont is a straight-A student with a future, and the whole thing was really an accident. Sasha convinces Lamont to confess to the crime, but she's not sure she really did the right thing. Allie Nardo visits Bosco's mom, Rose, at the bar where she works.

When Bosco finds out Nardo visited his mother, he confronts the small-time gangster. Nardo then sets Bosco up to look like he's taking a bribe. Bosco and Sasha come back at Nardo by setting him up to look like he betrayed his boss. Two of Nardo's buddies are killed in a classic mob hit, but Nardo himself gets away. Kim learns to gingerly handle her new Captain, Steeper, but none of the paramedics are pleased when Steeper says they're no longer allowed to hang out at the firehouse. Doc is in a strangely bouyant mood, and encourages Christian, Carlos's brother, to come on a ride-along with him and Carlos. Doc decides to have a party at his beautifully renovated house, which is a raging success, and he makes sure to tell everyone how important they are to him. Doc manages to seduce Sasha Monroe with his smile and a spontaneous kiss. Carlos feels judged by his brother for not being a "professional," like a doctor, but his brother is just proud that Carlos has found this new "family" of paramedics and cops in New York. Faith tells Bosco that she's coming back to work, even though she's not sure she's ready, but since the department doctor says she's ready and she doesn't want counseling on her record, she's going to do it. Faith tells Bosco to request that they be partnered up again, even though Bosco thought she wouldn't want to be anywhere near him.

Faith goes back to work even though Fred tries to convince her not to. Bosco lies to Faith that he talked to the boss about them partnering up again. When Faith finds out, Bosco tells Faith he can't be responsible for her getting hurt anymore, but Faith basically tells him he has no choice in the matter. A desperate Allie Nardo kidnaps Bosco in order to get Bosco to tell his fellow mob bosses that he wasn't a rat. Bosco does so, but they both know it's not really going to do any good. Nardo gives Bosco his mother back and commits suicide, asking Bosco to tell his family that he died like a man and didn't go into witness protection. Monroe wakes up at home, and not only is Doc gone, but her off-duty gun is missing too. Doc shows up late to work, wearing his dress uniform, and immediately shoots the annoying Captain Steeper. He threatens the rest of the paramedics, telling them not to help Steeper for at least 15 minutes, because that's how long people in this neighborhood would have to wait for medical help if Steeper closed down their house. Carlos, and then Kim, simply defy Doc and care for Steeper, trusting that Doc won't actually shoot his friends. The cops across the street become aware of the hostage situation in the firehouse, and ESU sets up snipers on the rooftops. Sully barely keeps Doc from getting shot in the head, and manages to talk the disturbed and tired paramedic into surrendering the gun and himself peacefully.

Kim, Carlos and Holly Levine go to mandated counseling to talk about what happened with Doc. Their counselor, Dr. Breene, becomes very concerned for their mental health and the fact that they have no outlet for their stress. Bosco's mom engineers a reunion between Bosco and his brother, Mikey. Mikey is finally off drugs, and is receiving his 6-month medallion from Narcotics Anonymous. As a gesture of goodwill, he gives Bosco and Faith some information on some Hassidic Jews who are dealing huge amounts of ecstasy. Bosco and Faith make a good bust, and Faith has fun rubbing it in Cruz's face. In the meantime, after a drug-dealer is murdered outside a rave, Cruz finds herself on the track of a drug-war between dealers of ecstasy with monkey faces on it, and dealers of ecstasy with dolphins on it. Cruz realizes that Mikey Boscorelli is dealing the dolphins, and set up the Hassids, who were dealing the monkey faces, using Bosco, so that he could get rid of the competition. Cruz tells Bosco, and Bosco is infuriated with his brother, even though he defends him to Cruz. Cruz tells the Hassids they were set up, and uses them to get info on Mikey. Cruz and her partner Dade go after Mikey, but Dade gets shot. Fred is furious with Faith for partnering up with Bosco again. Monroe is on a 30-day suspension for losing her off-duty gun.

Dade, although his vest protected him from most of the bullets, dies when his heart stops. A doctor later tells Cruz that it's because the bullets were spiked with liquid teflon. Cruz and the rest of anti-crime hunts for Mike Boscorelli as a cop killer. Bosco finds his brother and they have a heart to heart. Bosco tells Mikey that he believes that he didn't kill the cop, but says he has to take him in. Anthony Boscorelli, Bosco's dad, tells Cruz where to find his wayward son, and asks about a reward for turning in a cop killer. Bosco pleads with Cruz not to hurt his brother, and Mikey actually gives up Spider, the guy who really did the shooting. After a gun battle, the anti-crime unit and the cops of the 55 take down Spider. In the process, Faith saves Cruz's life, although for a moment Cruz thinks Faith is gunning for her. Cruz pisses of Jelly Grimaldi, who was investigating the murder of the dolphin-carrying drug dealer. Dr. Breene tries to convince the paramedics that they need to talk to someone about the trauma that they have been to, even if that someone isn't her. Fred still doesn't like that Faith is back at work and back with Bosco.

A new guy, J.D. Hart, joins the fire department. Everyone quickly learns about his past as a cop who testified against some of his fellow law-enforcers when Cruz picks a fight with him in the street. Sasha, who tries to to argue her way out of her suspension, rear-ends another car on the way home. The car bursts into flames, and a boy in the passenger seat of the car dies because of the air bags. Sasha is a mess, blaming herself for the boy's death. Thanks to some quick-thinking from new fireman J.D. and Sasha's friends on the force, it soon becomes clear that Sasha was trapped in an insurance fraud plan and is not to blame. Sasha still thinks God is punishing her for bending a few rules lately. Faith assures J.D. that Cruz is not popular, and that J.D. is okay in her book. Faith's family feels ignored at home when she gets wrapped up in cop life again. Sully and Ty take the LSATs together, even though Ty is late getting there because he was helping Sasha.

Bosco's brother, with a lawyer hired by his dad, tries to make a deal to become an informant for Cruz. Bosco doesn't want Mikey working with Cruz, so he tries to hook Mikey up with Sergeant Wynn in Narcotics instead. With the same tip from Mikey, Cruz and Wynn (and Bosco and Faith) all show up at a rave. Kim, who is getting a ride home from J.D. Hart, finds herself at the same rave when J.D. stops there to drop something off for a friend. Kids start collapsing from one tab of ecstasy, and J.D. calls an ambulance. At the arrival of the ambulance, Cruz decides to make her move, but Wynn pushes her aside. Faith and Bosco witness a guy throwing a molotov cocktail into the rave to start a dangerous fire, and they arrest him. Carlos and Levine, who were in the reporting ambulance, and Kim and J.D. try to usher out the drugged-up kids safely. Kim gets knocked unconscious, and when J.D. realizes she's not outside, he goes back into the burning building to save her. Kim disapproves of J.D.'s associating with the raver kids, and he resigns from the fire department. Faith is tempted to report Cruz to IAB. Getting separate tips, Wynn and Cruz both show up to bust the lead henchman of the monkey face crew, but during a car chase, Cruz runs the guy into a truck and he dies. Sully gets Ty to admit he's been spending a lot of time with Sasha and might be interested in her romantically.

Mikey's lawyer, Lester Martin, manages to get Mikey released on a technicality by ambushing and humiliating Bosco in court. Later, a 911 call brings Faith and Bosco to the Martins' home where their daughter, Rebecca, is unconscious, and her mother, Jan, is mildly hysterical. Jan says Rebecca choked, but when the doctor says that Rebecca was beaten, Faith arrests Jan. Jan screams for her husband and faints, and when the doctors treat her they realize she's covered in just as many bruises as her daughter. Faith explores the Lesters' apartment and finds strange squalid living conditions behind the elegant facade. Faith and Bosco arrest Lester for abusing his wife. Sully's favorite coffee shop proprietor is shot and killed during a robbery, and Sully goes after the perp personally. Sasha realizes Ty has feelings for her, and tells him that she's not ready for anything serious right now, but she can't help falling for his charming ways. Fred is colder and colder towards Faith, and Faith doesn't know what to do about it. Bosco is worried that Cruz is moving too fast on Mikey's information, and is putting Mikey in danger.

A new paramedic, Grace Foster, is transferred to the 55. She and Carlos immediately face off, and find they appreciate each other's attitudes. Sully and Ty discover a headless torso, and the body is finally identified as Bosco's brother, Mikey. Bosco is inconsolable, and tries first to blame Lester Martin and then Sergeant Cruz for Mikey's death. It turns out that Donald Mann, the father of Joey Mann (the drug-dealer that was killed in the car chase with Cruz, Bosco, Faith, and Sergeant Wynn) is behind Mikey's death, and he has more suffering in store for Bosco. Faith can't leave Rebecca's side, to the point of ignoring her own family for two days. Rebecca comes out of her coma. Faith finds out just how insane Jan Martin is, and that Rebecca was actually an illegal adoption, not the Martins' real child. Faith and Sasha hunt down Rebecca's real mother and engineer a happy reunion. Lester is arrested for kidnapping. When Faith finally gets home, she finds that Fred has left with the kids. Kim hasn't been feeling well, but blames it mostly on some bad Chinese food.

Faith talks to Fred about his leaving, and he admits that he's met someone else. Cruz tries to make peace with Bosco just before his brother's wake, but Bosco isn't interested. Carlos continues to pursue Grace, who's head-strong ways get on everyone's nerves. Jelly Grimaldi has a new suit. Donald Mann plans to have all the cops that he blames for his son's death eliminated during his son's funeral, and he gets some help from a cop on the inside. Cruz takes her anti-crime unit on a raid, except Yoshi says he wants to sit this one out because he wants to go to Bosco's brother's wake. Sergeant Wynn gets a tip and takes her narcotics team to the piers to bust Mann. Ty and Sasha, who are acting more and more like a couple, along with Sully and Faith, attend Bosco's brother's wake. At the same time, a bomb goes off in the apartment that Cruz is raiding, a bomb goes off on the pier where Sergeant Wynn's team is, and a car drives into the building where the wake is. Luckily, the driver of the car, who's wife is being held by Mann's people, doesn't get up the nerve to set off his bomb, and instead surrenders to the cops. Bosco's mother is seriously injured by the car, and Grace performs a tracheotomy in the field, for which Dr. Field says he'll have her license. Kim won't enter the building with the bomb because she's pregnant. Sergeant Wynn dies, but everyone else survives. At the hospital, the cops get together and figure out who's after them. When Mann finds out that Wynn was the only one of his targets that actually died, he sends an attack squad to the hospital to eliminate the offending cops once and for all. Cruz, Bosco, Ty and Faith are all together in the waiting room when one of the gunmen opens fire on them with a machine gun.