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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.

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.

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.

Although given up for dead by his doctors, McPike is revived into a comatose state by a distraught Vinnie. Meanwhile, Weiss and Boden remove incriminating evidence from the H.E.S. offices as they continue their search for Kousakis. Torturing and killing his driver, Boden learns of Kousakis' plan to be at the Jewish temple across from Father Patrick's church. Returning to the church, Vinnie unknowingly misses being killed as Kousakis decides instead to secretly leave his sanctuary for some food and supplies.

After abandoning McPike in Lynchboro, Vinnie calls in ex-agent Roger Lococco to help Frank finish his investigation of Volchek, without the knowledge or approval of the OCB. Afraid of what Vinnie might do in his state of mind, Frank has him listed as a rogue agent; a status which jeopardizes Terranova's life. Convincing his superiors to let him handle the case himself, Frank then gets Lococco hired as the new sheriff of Lynchboro.

After his complaints about the handling of hospital waste fall on deaf ears, Vinnie takes matters into his own hands. After beating up and robbing his boss, John Kousakis, he writes an anonymous letter to Emmet Soul, the state official charged with overseeing public health. Unknown to Vinnie, Soul has been taking bribes from Kousakis to overlook his operation. Meanwhile, Lococco convinces Frank that bringing down Volchek would have destroyed the town of Lynchboro.

Vinnie joins his old neighborhood friends for a bachelor party but ends up finding one of his pals in trouble with a loan shark

On orders from the Attorney General, Frank takes Vinnie into custody, while government agents apprehend Major Biggs and the counterfeit Yen for return to the United States. A closed door Senate hearing is arranged by the Attorney General to allow General Masters and Admiral Strichen to present their case against Terranova. Meanwhile, as she is being questioned by a Justice Department lawyer in preparation for the hearing, Kay Gallagher attempts suicide.

Lured to Utah by General Masters, Vinnie and Lifeguard locate the military depot where the Yen were printed, all the while being photographed by Major Biggs. Later, Vinnie and Kay meet with the billionaire hermit, Prescott Wilson, to ask why he commissioned Dr. Valenti's study and, again, are recorded on film by Biggs. Although Kay has records of phone calls and cancelled checks, Wilson denies any involvement and refuses to help derail Masters' plot. Meanwhile, Lifeguard learns of a large transport plane seen taking off from the depot two days earlier.

Under the pretense of getting a promotion, Vinnie has been summoned to Washington as part of an elaborate plan to avenge his meddling in the attempted overthrow of the Isle Pavot. Although warned by McPike that he is being used by power hungry politicians and lobbyists, Vinnie refuses to believe it. They attend a cocktail party where Vinnie sees an old nemesis from the Isle Pavot operation, Admiral Strichen. Vinnie is then introduced to Kay Gallagher, a young and powerful lobbyist. As they are getting acquainted, Strichen calls his boss, General Leland Masters, letting him know their trap for Terranova has been set.

When he discovers a box belonging to Vinnie's brother, Peter Terranova, the Monsignor from the parish delivers it to Vinnie. Among the items it contains, Vinnie discovers a gun belonging to his father, John, and a journal he kept chronicling his involvement with a local mob crew. Vinnie reads of his father's dissatisfaction with his life and wanting to do more for his wife and kids. Realizing his life is going nowhere, John approaches two friends, Angelo and Nick, and is invited to discuss working with a neighborhood Mafia crew. Vinnie reads about John's attraction to Teresa Dimonte, a girl from the neighborhood involved with Sam Roselli, a restaurant owner and mobster. Encouraged by Teresa, John takes up running numbers while working his bakery delivery route. However, when he finds Sam beating Teresa, John attacks Roselli. Warned his life is in danger for assaulting the mobster, John is encouraged by his friends to leave the country. Unwilling to run, he stays but starts carrying a gun for protection.

Having agreed to go undercover as part of his stepfather's Mafia family, Vinnie is running Aiuppo's organization while the Don is in the hospital. A turf war has broken out between Albert Cerrico and Joey Grosset as Albert learns that Joey has given some of his garbage collection business away in order to keep the peace with a Chinatown gang. When Albert and Vinnie go to visit Tommy Chin, an Asian gangster who is muscling in on business. Vinnie discover -an unusual sticky substance on Chin's stairwell which proves to be plastic explosive. Chin is manufacturing the explosives in his Chinatown building and selling it to terrorists around the world. McPike pressures Vinnie to expand his investigation in order to get both Chin and the Mafia.

Don Aiuppo arrives home from Italy and is shot while walking through his own greenhouse. Vinnie and his mom drive to the hospital with Aiuppo. Poochy, having recognized the body of one of the hit men, races to the home of Albert Cerrico and accuses him of ordering the hit. Just as Cerrico convinces Poochy that he didn't order the hit, Gene Gelb enters and announces that Boss Ziffo has been killed. Sensing that he and his family are next, Cerrico quickly gets everyone out of the house. Vinnie asks the OCB for protection for both his mother and Amber. He informs McPike that he will have to break his engagement to Amber.' On his way to-his car, Vinnie is nabbed by Poochy and Cerrico and taken for a ride. Cerrico accuses Vinnie of killing his step-father to in order to take over his position. Vinnie denies the accusation and states that Cerrico had the most to gain by the two murders. Cerrico swears his innocence and agrees to help get Vinnie into the next commission meeting.