Some time later Tommy, Paulie and a couple of nameless Salieri thugs truck out to a countryside farmhouse to pick up a shipment of Canadian liquor. Sam's supposed to be there waiting for them, but when Tommy and Paulie show up, things are strangely quiet. Tommy investigates, and finds one of Salieri's drivers dead in a truck. More than that, the whole crew's apparently been killed. The farm then erupts with Morello goons and corrupt cops, who've made a secret pact to bring down Salieri. They're also holding Sam - badly wounded and kidnapped again - in the loft of a barn. Tommy and Paulie eventually shoot their way through the soldiers and escape, with Tommy machinegunning their pursuers from the back of a truck. Once the three make it back to the relative safety of the city, Sam is dropped at Salieri's private doctor's house to recover, and Tommy limps back to Salieri's to deliver the news to the old man.
Of course, things are just beginning to go bad. It turns out that, while Tommy and his buddies were shooting their way through the farm, Frank quietly turned informant and handed Salieri's books over to the cops. The penalty is execution, and no flimsy "police protection" is going to hold back mob justice.
The task of hunting Frank down falls to Tommy, who's also ordered to retrieve the evidence Frank handed over. What's more, he's told to murder Frank with a sawed-off shotgun - apparently known in Sicily as a Lupara, a signature weapon for executions. After roughing up a couple of stoolies, Tommy figures out where Frank is hiding and follows him to the airport, where - after shooting his way through what feels like dozens of heavily armed G-men - he discovers that Frank's only reason for turning traitor was because Morello was holding his wife and child hostage. If Frank cooperated with prosecutors, however, he and his family would be flown to safety in Europe.
Once again, Tommy can't bring himself to commit cold-blooded murder, especially not after hearing a story like that. After Frank leads him to Salieri's books are safe, Tommy orders Frank to get on the plane to Europe and never breathe a word of his existence to anyone. Convinced that Tommy killed Frank and disposed of the body, Salieri holds a full funeral in the man's honor.
The heat's not off yet, though; Salieri has to completely disrupt the prosecution's case. While Sam and Paulie are sent out to take care of witnesses, Tommy is tapped to sneak into the prosecutor's mansion - which is crawling with armed guards - and crack a safe to steal back the last shreds of evidence the state has against Salieri. Succeeding with the help of safecracker Salvatore, Tommy hightails it back to safety and celebrates with the rest of the gang.
Some time after that, Tommy marries Sarah and the two have a daughter. Prohibition ends, and Salieri's family uses the money it made running booze to fund legitimate business deals - while still running illegal rackets behind the scenes, of course.
A couple of years later, Tommy and Salieri head out for lunch after Salieri's bodyguard calls in sick. During the meal, a group of Morello thugs drive up and start shooting up the restaurant before tossing in a grenade - killing just about everyone except Salieri and Tommy, who've taken cover behind an overturned table. Unharmed, Salieri distracts the goons while Tommy sneaks around, outflanks them and guns them down.
Furious at the attempt on his life, Salieri realizes that his bodyguard sold him out, and he and Tommy immediately pay a visit to the man's apartment. Catching him in his underwear and storming past his sobbing wife, the mobsters chase the man into a courtyard, where they blow his brains out in front of his neighbors. Being civic-minded people, some of those neighbors respond to the screams of "murder!" by attacking, forcing Tommy to kill them as well.
Meanwhile, Morello is surprised to learn that the assassination attempt failed. After consulting with his brother Sergio, he prepares for all-out war against Salieri.
Salieri and Tommy aren't resting, either, and decide it's time to take the fight to Morello. First, though, they need to weaken him and draw him out, which they decide to do by taking out his strongest allies. First on the list is a certain pain-in-the-ass city councilman - you know, the one with the dead son? To kill him, Tommy has to infiltrate the man's birthday party, held on a steamboat anchored near the city's Central Island.
Disguising himself as a crew member, Tommy sneaks aboard and finds a gun hidden in a restroom - which, in a twist that keeps it from being just another Godfather reference, has been fouled by a mess so disgusting that Tommy has to actually clean it before he can even look for the gun. He finds it in time for the councilman's speech, though, and as he finishes addressing his guests, Tommy walks up and executes him in front of the crowd. Chaos ensues, and Tommy escapes on a speedboat piloted by Paulie.