Vinnie (Ken Wahl) is released from prison where he has been for two years to establish his cover. He meets his boss, Frank McPike (Jonathan Banks) and gets to see his coach and mentor, Jerry Greco (Robert Miranda). Greco is killed and Vinnie demands to be put in to finish the investigation. He uses his ingenuity to get a foothold in the Steelgrave crime family, but it will take a while to finish this job.
Vinnie and Sonny's right hand man, Tony Grecco, have a run-in with the cops for which Vinnie is arrested. The Steelgraves find that guns are being exported illegally using their pier and decide to take possession of the guns and sell them back to the owner. The meeting goes down bad and ends with Dave Steelgrave's death. Vinnie gets rid of Tony by setting him up and having him arrested. To prove his loyalty, Vinnie shoots a federal agent for Sonny (but the agent was warned, wore a bullet proof vest, and was then moved out of state).
After "making his bones," Vinnie moves up in the Steelgrave family when Sonny gives him Tony's old waterfront action. The pressure is on Sonny when "Pat the Cat" Patrice insists on installing accountant Sid Royce in the office to keep an eye on his interests, and to balance the power, Philly's "No Money" Mahoney insists Sonny find a place for his man, Harry "the Hunch." As if he doesn't have enough to worry about, there's a new district attorney who plans to make a name for himself by bringing Sonny down. Sonny and Vinnie are arrested for attempted murder when someone shoots at the DA and throws the gun to Sonny.
While trying to regain control over the men running his ghetto drug operation, Sonny gets a call from Italy asking him to take in his nephew and teach him the business. After getting into a fight with Lorenzo, Vinnie has Frank do a check and it turns out the guy is really an insane mass murderer who killed the real Lorenzo before coming to the States. Frank and Pete both warn Vinnie to break off his budding romance with Gina, the widow of a crooked cop who killed himself. Vinnie and Lorenzo have a showdown after Lorenzo rapes Gina, ending with Vinnie killing him.
Vinnie nearly blows his cover when he becomes obsessed with finding out who killed his cousin, causing Frank to threaten him with dismissal. Frank desperately wants Vinnie to concentrate on nailing the Zaratzos, who are trying to arrange a drug smuggling deal with Sonny, because they killed one of Frank's agents.
After several deals go sour, Sonny starts suspecting Vinnie may be a plant. Frank orders Vinnie to drop the case when he finds out the local police have an informer in Sonny's operations. Sid has Frank picked up and tortured, but Vinnie and undercover cop Karen Malloy rescue him. Karen's disappearance points the finger at Sid as the leak.
Vinnie decides he must tell his mother the truth about his work when she is hospitalized after being mugged. Frank has Lifeguard bug Carlotta's hospital room, then has a change of heart when Carlotta charms Sonny by telling him how much Vinnie loves him. Vinnie's admiration for Sonny lessens when his own informal investigation into his mother's mugging leads directly back to Sonny's empire.
When Sonny refuses to let Joey out of his contract, the singer goes to Mahoney to ask him to speak on his behalf. Mahoney tells Sonny he's losing his power, so Sonny has two crooked cops rough Joey up, unaware that one of them is a loose cannon who crushes the singer's voice box. After Frank interrogates them, the cops follow Frank and get pictures of him meeting with Vinnie, which they plan to sell to Sonny. Since Vinnie is now acting as Sonny's "right hand," Joey Bags insists that he be formally initiated into la famiglia. A confrontation between Joey, the cops and the mob bosses ends up with Joey and the cops dead, and Frank switching the photo of him and Vinnie with one showing him meeting with Patrice.
A staged argument between Sonny and Vinnie prompts Patrice to propose that Vinnie leave Sonny and come to work for him. Sonny is busy planning his wedding to Theresa while keeping an eye on the growing power struggle between him and Patrice. After Patrice tells Vinnie he's going to hit Sonny in the morning, Vinnie arranges for Frank to arrive before the scheduled time to make the arrests. Sonny kills Patrice at his bachelor party, then demands to know why Vinnie didn't tell him about the hit.
While Vinnie tries to reassure Sonny of his loyalty, Aldo calls to warn Sonny the cops are on the way, causing Sonny to flee, with Vinnie right behind him. They end up locked in a closed theater where they fight, drink and try to justify their lives. Meanwhile, Frank is distraught over Vinnie's disappearance as he tries to get information from the other mob bosses. After he finds out Vinnie's location, he arranges a rescue, which culminates in Sonny committing suicide and Vinnie being arrested to protect his cover.
Distraught over the guilt he feels over Sonny's death, Vinnie is ordered into therapy. Pete hears the confession of a man with a contract out on his life, and is torn between his vows and giving Vinnie the information he needs to help the guy out.
Frank wants to get Vinnie back on the job, so he assigns him to a routine case investigating hit man Roger Lococco, unknowingly dropping Vinnie into the middle of a case that has international repercussions. After winning Roger's confidence, Vinnie is asked to work for Mel and Susan Profitt, a brother and sister team who run a worldwide drugs and munitions organization.
Convinced an associate's bride-to-be is a Fed, Mel insists he postpone the wedding. Insulted, Paco brings up a death squad to hit Mel, then arranges to kidnap Susan to force Mel to give him all of their drug action. Vinnie and Roger rescue Susan. Frank finds out Paco's bride was an undercover CIA agent.
Vinnie has second thoughts about the case and tells Frank he wants out. When he goes to Mel to resign, Mel offers him a chance to take over his worldwide drug operation. The catch: Vinnie must go to Tennessee and take it back from the middle men who have seized control.
Mel's desire to buy a baseball franchise is two-fold: he wants to play on it, and he wants to take it away from an old business associate who cheated him in a Mexican drug deal. Vinnie is fighting his growing feelings for Susan while trying to discourage Jacqueline from getting involved again with all the debauchery on the Hotei.
When some of his munitions contacts begin drying up, Mel decides to blackmail a French Deputy Minister of Defense into supplying him with the weapons he needs. After setting Vinnie up to be arrested for espionage, Susan makes it up to him by letting him go to bed with her. When Vinnie mysteriously comes up with the documents Mel needs, he arouses Roger's suspicions.
Hiding out in Vancouver after the fall of the Steelgrave empire, Aldo Baglia sees a photo of Vinnie in the paper and decides to even the score, sending Vinnie into a coma from two serious gunshot wounds. Roger, using his CIA contact, tracks down Aldo, but Aldo accidentally falls off the roof of a building before he can answer any questions. Upset about Vinnie being shot and his wife leaving him, Frank falls into the arms of a pretty CIA agent.
After his munitions operation starts falling apart, Mel orders Vinnie to set up a meet with the mob to use his immense cocaine trade to regain financial power. Still suspicious of Vinnie, Roger has Herb check him out and learns that Vinnie is working for the OCB. Vinnie takes Mel to Don Aiuppo, who arranges for the drug trafficking to be overseen by two "third generation" gangsters who will stop at nothing, including threatening Carlotta, to insure the deal doesn't fall through.
With Herb becoming more insistent about their agenda, Roger schemes to get Mel to fund the military coup of Isle Pavot. Unfortunately, Mel is convinced that Cabra, the man Herb wants to put into power, has put a voodoo curse on him and orders Vinnie to find a woman who can remove the curse. Realizing that Mel is a major stumbling block to the mission, Roger sends him over the edge by smashing the crystal that contains Mel's soul. Despondent, Mel asks Susan to kill him, and she does.
Susan is arrested for Mel's murder and while she's in jail, she tells Vinnie she's pregnant with their baby. Roger sets Vinnie up for Mel's murder, then sets about driving Susan mad so he can gain control of her vast fortune to fund the Isle Pavot coup. Frank trails Roger to Herb. Vinnie finds out Susan isn't pregnant. Susan goes insane and has to be institutionalized.
With Mel and Susan out of the picture, Frank considers the case closed. However, Vinnie wants to find out where Roger fits into it all and goes to Vancouver to find him, but instead, he witnesses Preet's murder and links it to Herb. Frank and Vinnie go to Stockton, where Roger is training mercenaries for the coup. Roger kidnaps Frank and tells Vinnie he'll be released after the operation, then Vinnie tells Roger that Herb is using him. Roger overhears Lelond assuring a major corporation that they can get all the cheap labor they need once he takes over Isle Pavot and realizes the coup is just an excuse for Herb to regain acceptance in Washington. Roger works with Frank and Vinnie to set up Herb and sabotage the coup.
Vinnie and Roger are subpoenaed to testify at a Senate hearing concerning Ketcher and the failed overthrow of Isle Pavot, but Vinnie balks at McPike's orders that he testify as a hood and not as an OCB agent. Roger testifies, then demands to be released from protective custody after an attempt on his life. When Roger is killed in a mysterious boat explosion, Vinnie testifies anonymously and substantiates Roger's testimony that Herb was responsible for everything. Abandoned by everyone in Washington, Herb is approached by the Soviet Union to defect, but he kills himself instead. Tired of all the lies, Vinnie resigns from the OCB. Roger "reappears" to let Vinnie know he faked his own death to escape the CIA.
After resigning, Vinnie returns to his old neighborhood to try and get some peace after his life undercover, but is distressed to find white supremists are stirring up trouble. Daryl Elias is promoted to OCB director and orders Frank to either bring Vinnie back to work, or in for debriefing. After a synagogue is trashed, Pete speaks out against the white supremists and is then murdered in a hit and run accident, making Vinnie rejoin the OCB to find his killer.
Vinnie hesitantly goes back to work for the OCB under the promise they will help find Pete's killer, but Daryl is more interested in getting his star agent to work on a "real" assignment. Ritchie digs himself in deeper with the Pilgrims of Promise when he uses Vinnie's car to help rob an armored car. Depressed over Pete's death, Vinnie turns to Angie for consolation, but they both agree they don't want to risk their special friendship by becoming lovers. Vinnie talks Daryl into giving him weapons to sell to the Pilgrims, then he throws the bust when he sees they have Ritchie with them.
Unbeknownst to Vinnie, his car was used in the robbery where an off-duty cop was killed, leading to his arrest and brutalization at the hands of the NYPD. Frank bails him out, then reluctantly lets Vinnie continue his pursuit of Knox Pooley. Vinnie tells Ritchie he's a cop and asks him to help him gather evidence against the Pilgrims. Vinnie goes to a Pilgrim rally and stumbles across the truck that was used to kill Pete, then agrees to a meet with Stan in the hopes of tying Pooley to it, leading to Stan and Ritchie's arrests.
Knox Pooley realizes Calvin is insane and kicks him out, causing Calvin to go off the deep end and take a famous black leader hostage. Richie becomes disenchanted when he realizes Pooley was only in it for the money. Paul Beckstead takes over as director of OCB when Daryl cracks under the pressure and is dismissed for making obscene phone calls.
Vinnie is questioned about his connection to Don Aiuppo, thus learning his mother is dating the retired mobster. Checking into it, he finds Rudy and Carlotta were in love as teenagers, then is stunned when Rudy proposes and she accepts. Mark digs up information showing that Rudy is in the country illegally and sets him up to be deported, not knowing it means that Carlotta will leave, too. At the last minute, Rudy changes places with his brother, Tito, who wants to return to Italy.
When garment manufacturer Eli Sternberg cannot get a loan to bail out his business, he turns to mobster Ricky Pinzolo for the money. David goes to the OCB for help when he finds out Eli is in debt to the mob. Vinnie meets with David, then reluctantly agrees to take the case, running into opposition from Eli, who doesn't want a hood working for him. Pinzolo demands that Vinnie keep him apprised of everything going on. Vinnie wins Eli's trust when he gets a delayed shipment released from customs.
Eli impatiently awaits news from Sri Lanka, where a terrorist's bomb exploded at David's hotel. Vinnie is hit by a taxi, and Frank talks John Henry Raglin into taking over the case when he learns that Vinnie can't return to work for awhile. Eli speaks out against Pinzolo at a fund raising dinner. Pinzolo visits Vinnie in the hospital and Vinnie suggests his partner can take over for him, opening the door for Raglin.
Raglin follows Pinzolo's crooked trail into Chinatown, where a garment-worker's strike has snarled an important order for the Sternbergs. Meanwhile, Eli's niece Carole sews up her alliance with Pinzolo. Raglin tries to get Maxine Tzu to realize the strike isn't helping, and they end up in a tryst.
Raglin uncovers evidence that Carole is working with Pinzolo to bankrupt Eli. David confronts Pinzolo and forces him to take him to the bank to give him the money he cheated Eli out of, culminating with David getting killed as a suspected robber. David's death sends Raglin into a tailspin, digging up memories of a past case where another innocent bystander was killed.
Raglin pursues a lead that David left him about Pinzolo's murderous past, but they can't find the body. Eli offers Raglin money to kill Pinzolo. Raglin urges Frank to get Carole to testify against Pinzolo, but she has been killed. Revealing that the reason he quit undercover work is because he was tortured into giving up two fellow agents, Raglin vows to bring this case to a successful conclusion. Deciding things are getting too hot for him in the States, Pinzolo plots an escape to Morocco. Raglin confronts Pinzolo at the airport, and when Pinzolo figures out Vinnie is a cop, Raglin kills him.
Frank shows up at Vinnie's house in the middle of the night and states than his wife is dying and he can't afford the liver transplant she needs to save her life. Vinnie leaves a box containing a million dollars on the front seat of Frank's car. Frank confronts Vinnie about the money and Vinnie confesses it's money Roger gave him as a parachute in case he ever needed to bail out of undercover work. After arguing with Vinnie about the ethics of using the money, Frank finally decides he'd rather save Jenny's life, so he pays for the operation. Frank and Vinnie turn themselves into Paul for using the money, but Paul dismisses it when he can't find any record of Roger or the money in his files. After Jenny recovers, she tells Frank that their stale marriage is what almost caused her to die, so she insists he move out before she gets home from the hospital.
Concerned that Vinnie is addicted to the pain pills he's been taking for his leg, Frank calls in Paul Beckstead, who orders Vinnie to undergo a routine physical exam. At the hospital, Daryl Elias is undergoing therapy and, holding Vinnie responsible for his downfall, he accesses Vinnie's file and orders that he be held for psychiatric evaluation. When Vinnie resists, he is sedated and locked up against his will. While in his drug-induced twilight zone, Vinnie's worst nightmare comes to life in the form of Sonny Steelgrave, who blames Vinnie for his death.
Frank exchanges Pinzolo's jet with the DEA for a small record company, then allows Vinnie to run it. Bobby Travis talks Vinnie into hiring him by promising Vinnie he'll teach him all he needs to know about the business. Getting caught up in the glamour, Vinnie decides he's going to revive Diana's career by having her cut a record.
Despite Paul Beckstead's misgivings, Vinnie uses Diana's record to start a bidding war in the hopes of selling Dead Dog to a bigger label. When Vinnie signs elusive James Eliot, Newquay offers to buy Dead Dog without Vinnie, Bobby or Diana. Diana balks at Newquay's offer, revealing they used to be lovers. Contrary to Frank's wishes, Vinnie sells Dead Dog to Isaac. Frank warns Vinnie that Newquay has been digging into Vinnie's past.
Vinnie bails artist Monroe Blue out of jail, then tells him to help Diana work on some songs. Vinnie begins to wonder about Isaac's honesty when he gets a $57,000 bill for bogus record returns. Winston crashes Diana's party to show off Eddie Tempest. Diana succumbs to Winston's charms, then tells Vinnie she has to get out of the country to get away from him. When Vinnie gives Diana money to leave, Winston demands to know where she is, getting furious when Vinnie refuses to tell him.
Sensing Eddie's unhappiness with Newquay, Vinnie tries to lure him away by promising him he can work with Monroe. Winston finds out and has Medley thrown off a roof as a warning to Vinnie. Bobby travels to Japan and finds evidence that Twine may be cheating him and Vinnie. Isaac loses Shakala to Newquay in a crooked poker game. Frank talks Isaac into helping him gather evidence against Newquay.
Amber talks Winston into letting her and Isaac run Shakala at Radiance. Feeling like he's at a dead end, Vinnie urges Bobby to make his own way inside Radiance while he starts turning up the heat under Winston. Isaac agrees to dig up information for Frank. Vinnie urges Claudia to take a more active part in Radiance. Eddie is furious when the check he uses to buy his mother a house bounces. Claudia begins an affair with Eddie, and both are killed when they fall through a skylight.
Winston serves Vinnie with an order to vacate, which Vinnie counters with the vow that he's going to stay at Radiance for the duration of his contract, causing Winston to dig deeper into Vinnie's past. Winston orders Vinnie and Bobby to work in the mailroom. Bobby uncovers Vinnie's file, which was sent to Winston, and confronts Vinnie about being a cop. Winston is arrested when he agrees to buy the illegal tape of Eddie from Isaac.
Just as Frank's suspected, the case against Winston is thrown out of court as entrapment, pushing the investigation back to square one. Vinnie urges Bobby to start working away at Winston from inside Radiance by contacting all of the acts and showing them how badly Winston has been ripping them off. Isaac suffers a massive heart attack and later dies. Winston goes mad. Bobby gets Dead Dog. Amber gets Shakala back.
Wrapping things up at Shakala, Frank reminds Vinnie that they're scheduled to go fishing in the morning. Vinnie and Amber go to dinner, stay up all night talking. Vinnie is surprised to find they're going fishing with Lifeguard, who is in an emotional struggle over his daughter's plans to marry. Frank, Vinnie and Dan have a long talk about relationships around the campfire. Dan agrees to meet his future son-in-law. Frank tries to reconcile with Jenny. Vinnie decides to go after Amber.
Vinnie warns Amber about her lawyer, but Amber thinks he's just jealous. Vinnie runs into an old high school buddy who urges Vinnie to pursue Amber. Vinnie uncovers proof the lawyer is conning Amber into selling Shakala. Amber and Vinnie fall in love.
Carlotta and Rudy Aiuppo return to the States when they hear about Amber. Carlotta thinks Amber isn't right for Vinnie. Rudy takes Vinnie to the Commission and tells them that Vinnie is under his protection, even though he's not in the business. Frank is overjoyed to learn that Vinnie has been introduced to the Commision. Vinnie tells Amber he's a cop and proposes to her. Rudy is shot, forcing Vinnie to become embroiled in a brewing mob war.
While keeping vigil over Rudy, Vinnie learns that Grosset's father-in-law was also hit, setting up a power struggle within the mob. Albert courts Vinnie's alliance by letting him in on his plan to smuggle millions of dollars worth of heroin into the country. Vinnie goes to the Commission and demands Rudy's seat at the table.
The tension mounts between Cerrico and Grosset over control of the garbage collection business. Grosset forms an uneasy alliance with Chinatown mobster Chin. Carlotta urges Rudy to get better and get Vinnie out of the middle of the impending mob war. The OCB closes down the explosives factory in Chinatown. Gina Grosset kills Chin. After an assassination attempt at the opera, Amber tells Vinnie to move out.
Frank wants to pull Vinnie off the case when he finds out that D.A. Peter Alatorre plans to expose Vinnie as the head of the Commission in a news conference. Albert is distraught when his son is expelled from school because of his recent press coverage. Rudy calls Alatorre to his hospital room to show that he is back in the country, taking the heat off Vinnie.
Rudy discovers Joey's plan to kill him, Albert and Vinnie, so sets his own plan into operation by convincing Albert he must kill Grosset. Albert and Joey have a showdown that ends with Joey dead and Albert in jail for his murder. Wanting her due, Gina sets up a meet with the Commission to offer them Albert's heroin deal. When Frank easily affects the arrest of the Commission, Vinnie begins to suspect that Rudy set everything up for them.
Frank and Dan urge Vinnie to try and reconcile with Amber. At their urging, he goes to her, they make love, then she demands that they see a counselor. Following their therapist's advice, they go away for the weekend, where they both realize they're too involved in their careers to be able to maintain a relationship with each other.
When a local priest finds a box that belonged to Pete, he takes it to Vinnie, who finds a diary of his father's inside. As he reads it, he finds out about a dark episode involving his father and the local mob. The episode uses black and white film and familiar faces to bring John's diary to life.
Vinnie and Frank try to cheer up Dan, who's depressed about becoming a grandfather. When Lauren finds a phony check in her husband's pocket, she asks Dan to investigate, and he uncovers a scam a local builder is using to bilk his insurance company. The builder is shut down, throwing Stephen out of a job and making him decide to leave town.
Vinnie attends his 15-year high school reunion and bumps into two old friends, one a mob lawyer and one a detective. Vinnie is torn between telling Denise he's a cop and protecting his cover. Frank tells Vinnie that Denise has bugged his house, making Vinnie furious and determined to teach Denise a lesson. Denise and Mooch get married.
Vinnie is called to Washington to investigate a counterfeiting operation designed to sabotage the Japanese economy. Frank warns Vinnie to be careful, that there is some kind of power play going on, because Paul was mysteriously sent to Thailand, leaving Mark in charge. Vinnie suspects Masters wants to set him up for throwing the coup of Isle Pavot. Mark is relieved of duty when he loses control after his former mentor is murdered. Vinnie meets Kate Gallagher.
In the aftermath of economist Valenti's assassination, new paths open in Vinnie's investigation of the plot to disrupt the Japanese economy. Although Vinnie strongly suspects that Masters is behind the plot, he follows the trail Masters sets out for him. Vinnie and Kate both go to Utah to track down the mysterious Mr. Wilson.
Vinnie and Dan find evidence of the counterfeiting ring in Utah, but it seems to have come too easily, so Vinnie heads into the mountains to meet a billionaire recluse, Prescott Wilson, who might hold the key to the truth in the case. Frank and Vinnie convince Senator Pickering to delay passage of Senator Getzloff's trade bill while they search for the plane carrying the yen. Masters presents the Attorney General with photos of Vinnie and Kate talking with Wilson, as well as the printing plate with Vinnie's prints on it. Frank is ordered to arrest Vinnie.
Vinnie is the fall guy in the alleged plot to disrupt the Japanese economy, prompting the Attorney General to launch a classified Senate investigation that could cost Vinnie his badge. Fearing her career is ruined, Kate attempts suicide. After hearing all the evidence, the Attorney General relieves Vinnie of his duties, stating there's enough to prosecute him for treason. Prescott Wilson arrives and places all the blame on Masters. Masters goes off the deep end and kills Strichen. Vinnie is cleared of all charges.
During a budget meeting, Frank gets a call from Jenny that his father is causing trouble at the rest home he's at. Frank takes Mike home while he looks for a new home for him. Mike tells Frank he's not going to leave until Frank reconciles with Jenny. Vinnie takes Mike to a bar for lunch and the old man gets them into a brawl. Jenny reluctantly agrees to have dinner with Frank and Mike. Mike realizes Frank and Jenny aren't going to get back together, so he allows Frank to find him a new rest home.
Steelgrave's former accountant, Sid Royce, is suffering in the Witness Protection life Frank assigned him. When his wife leaves, he snaps and decides to get revenge against Frank for destroying his life. Jenny agrees to have dinner with Frank, then invites him back home. Their romantic evening is destroyed when Sid pulls a gun on them. Jenny talks Sid into letting Frank go by convincing him she's his missing wife. Frank kills Sid in front of Jenny, ending whatever chance they might have had at reconciling.
Feeling lonely, Vinnie joins his old buddy Mike Caccatori at the bachelor party for their high-school friend Jimmy "The Legend" Vitale, but the trio's friendship is put to the test when Jimmy reveals that he's broke and owes money to a loan shark. It ends up being a dream.
Frank's reporter friend tells him about a corrupt town in Washington, spurring Frank to assign Vinnie to the case. Vinnie sets his cover as a truck driver whose rig just got repossessed. The local sheriff investigates Vinnie and finds out he used to be a cop, so he offers him a job as deputy. Vinnie prevents Bobby from killing Volchek, then fakes Bobby's death to win Volchek's trust.
When the bodies of two missing deputies turn up, it points to a serial killer who has been terrorizing the northwest. Volchek assigns the investigation to Vinnie when Stem loses control. Frank warns Vinnie he has to leave after Dan tells him there's a 40 man task force on the way to Lynchboro. As Volchek tries to eliminate possible suspects, Stem confesses to the murders, then electrocutes himself. Vinnie flashes back to Sonny killing himself, then snaps and takes off, stealing Frank's car.
Vinnie calls in Roger Lococco to take over the case, then holes up in a seedy hotel in Seattle. Frank is more interested in looking for Vinnie than in nailing Volchek. Paul orders Frank to continue the case and offers him another agent, which Frank refuses. Roger takes over as sheriff. Dan moves to Seattle to support Frank and look for Vinnie.
Vinnie takes a job hauling hospital waste as he continues to hide out in Seattle. Frank finds out Volchek is going to bribe a state official to get the license for his hospital and plans to arrest them after dinner. Roger uncovers Volchek's cryogenic vault. Lacey talks to Roger about how important Volchek is to the town, causing him to throw the arrest.
Volchek becomes depressed over losing the hospital. Roger and Frank try to save Lynchboro by getting Volchek to realize he really is in control. Vinnie goes to Kousakis when he realizes the waste they're dumping is causing a hepatitis outbreak in a nearby school, then attacks Kousakis when he tells Vinnie to mind his own business. Vinnie tries to alert an official to the toxic waste, but it turns out the guy is corrupt and tells Kousakis to kill Vinnie. Feeling trapped, Vinnie kills the two gunmen sent to kill him, then flees into the night. Roger leaves, telling Frank to tell Vinnie they're now even.
Depressed, Vinnie contemplates suicide, then hears church bells. He goes to confession and breaks down, begging Father Pat to help him. Frank goes to Seattle to look for Vinnie. Vinnie tells Father Pat about the toxic dumping, and the priest arranges a press conference. Frank finally finds Vinnie at the church. Kousakis overhears the plan to expose him on the news and shoots at them, wounding Frank and Father Pat. Vinnie and Dan chase Kousakis. Dan finds out Frank is in critical condition and goes to the hospital. After trying to revive Frank, the doctors give up when he flat lines.
Frank has an out-of-body experience, then briefly awakens when he hears Vinnie calling him. Kousakis kills Harriet, then hides out at the church while waiting to kill Boden. Vinnie decides to try repairing the church bells in the hopes that they will awaken Frank from his coma. Vinnie discovers Kousakis in the bell tower, but Kousakis jumps to his death before Vinnie can summon the police. Vinnie repairs the bells and rings them, waking Frank.
While Frank is in Washington to talk to Paul about returning to work, Dan calls to say Vinnie missed his last check-in. Frank goes to Vinnie's house and finds evidence that he was kidnapped. Despite Paul's objections, Frank begins his own investigation, finding out from Carlotta that Vinnie was looking into the death of a priest in El Salvador. Frank follows the trail to Miami and Michael Santana, a disbarred Federal prosecutor, and the last person Vinnie contacted. Santana refuses to help Frank, saying he doesn't know anything about Vinnie's disappearance. Digging deeper, Frank stumbles upon a CIA investigation and is ordered to back off.
The arrival of a shipload of Haitian "boat people" in Miami inadvertently interferes in Santana and McPike's plans to catch Guzman in an illegal act, and opens up a new case.
Santana impresses Guzman with his trustworthiness and finds himself getting deeper into Guzman's operations, a move that endangers his father and Dahlia.
Santana learns the details of Guzman's money laundering operation and comes face to face with the drug lord who cost him his job as a Federal prosecutor.
Arnado Guzman, hiding out in El Salvador, contacts his trusted "son," Michael Santana, to bring him funds, and Santana concocts a plan to bring him back to justice.
When his brother-in-law disappears, Santana is drawn into a web of police corruption.
Hillary asks Frank and Santana for help in a lawsuit involving defective aircraft parts.
Santana goes after a group of high school drug dealers who shot his niece after she witnessed the murder of her high school principal.
Vinnie Terranova is back, foiling a staged kidnaping of computer mogul Paul Callendar's son in order to probe possible inside information brokering. Meanwhile, McPike is having a hard time working with his young boss, who feels Terranova and McPike are dinosaurs not worth supporting.
