In 1998, Leone mobster Antonio "Toni" Cipriani (Danny Mastrogiorgio), forced to live abroad for four years following his murder of a made man, returns home to Liberty City. His boss, Don Salvatore Leone (Frank Vincent), welcomes him back and assigns him to work under another Leone mobster, Vincenzo "Lucky" Cilli (Joe Lo Truglio), who despises Toni, and a former member of the Sindacco family looking to switch allegiances, JD O'Toole (Greg Wilson). At the same time, Toni finds that his mother (Sondra James) disapproves of his low rank in the Leone family, and is forced to stay away from her when she calls a hit on him. After Toni escapes being arrested on a job, he quickly discovers Vincenzo seeks to take his place within the Leone family. Vincenzo later leads Toni into another ambush to be killed, resulting in Toni escaping the trap and killing Vincenzo in revenge. Following Vincezo's death, Salvatore begins to personally assign work to Toni, including looking after his trophy wife Maria (Fiona Gallagher).
Toni soon uncovers evidence that Sicilian Mafia underboss Massimo Torini (Duccio Faggella) is orchestrating plans for minor gangs to take control of the Leones' territory, whilst they're engaged in a war with the Sindacco and Forelli families. After helping to escort Salvatore downtown as problems arise, Toni earns his trust and becomes a made man within the Leone family, causing his mother to call off the hit on him. Toni soon finds himself entrusted with killing the city's mayor, controlled by the Forellis, and assisting media mogul Donald Love (Will Janowitz) into becoming his replacement. However, Donald goes bankrupt after losing to his rival Miles O'Donovan (John Braden), who promptly has Salvatore arrested on several charges soon after his election. Toni remains loyal to Salvatore, and continues to take jobs from him in prison, including killing Don Paulie Sindacco (Jeff Gurner) as revenge for having Salvatore arrested. Meanwhile, Donald also enlists Toni's help in rebuilding his fortune, and hires him to destroy the Forelli-controlled district of Little Italy in Fort Staunton with explosives, so that Donald's company would receive city funding to redevelop it.
With the Leones now the most powerful and sole-surviving Mafia family in Liberty City following the Sindaccos and the Forellis' defeat, Salvatore finds himself targeted by his rivals, forcing Toni to protect him before his trial. Upon being released on bail, Salvatore quickly deduces that Torini organised the mob war and rigged the mayoral elections. Suspecting Torini will likely kidnap Mayor O'Donovan to prevent him from dropping the charges against Salvatore, he joins Toni to rescue him and Toni proceeds to kill Torini. In return, Salvatore demands that O'Donovan grant his family protection, which he reluctantly accepts to do. Shortly after, Salvatore reveals to Toni that Torini was working for his uncle (Bruce MacVittie), who wanted to weaken his nephew's control over the city as revenge for not paying him tribute. When Salvatore and Toni confront him, Uncle Leone admits defeat and decides to leave for Sicily for good. With his uncle no longer a threat, Salvatore settles in with controlling the city, while Toni is promoted to caporegime as repayment for his assistance.
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