In 1846, in Lower Manhattan's "Five Points" district, a territorial war raging for years, between the "Natives" and recently arrived Irish, Catholic immigrants, is about to come to a head in Paradise Square. The Natives are led by William "Bill the Butcher" Cutting (Daniel Day-Lewis), an American Protestant nativist, with an open hatred of recent immigrants. The leader of the immigrant Irish, the "Dead Rabbits", is Priest Vallon (Liam Neeson), who has a young son, Amsterdam (played as a child by Cian McCormack). Cutting and Vallon meet with their respective gangs in a horrific and bloody battle, concluding when Bill kills Priest Vallon, which Amsterdam witnesses. Cutting declares the Dead Rabbits outlawed and orders Vallon's body be buried with honor. Amsterdam seizes the knife that kills his father, races off and buries it. He is found and taken to the orphanage at Hellgate.

Sixteen years later, Amsterdam returns to New York as a grown man (Leonardo DiCaprio) in the second year of the Civil War. It is September 1862, days after the Battle of Antietam and the announcement of the Emancipation Proclamation. Arriving in Five Points, he reunites with an old friend, Johnny Sirocco (Henry Thomas). Johnny, now a member of a clan of pickpockets and thieves, introduces Amsterdam to Bill the Butcher, for whom the group steals. Amsterdam finds many of his father's old loyalists are now under Bill's control, including Happy Jack Mulraney (John C. Reilly), now a corrupt city constable and in Bill's pocket and McGloin (Gary Lewis), now one of Bill's lieutenants. Amsterdam soon works his way into the Butcher's inner circle. Amsterdam learns that each year, on the anniversary of the Five Points battle (February 16), Bill leads the city in saluting the victory over the Dead Rabbits and he makes plans to kill the Butcher during this ceremony, in front of the entire Five Points community, to exact public revenge. Amsterdam meets Jenny Everdeane (Cameron Diaz), a pickpocket and grifter. Amsterdam is attracted to Jenny (as is Johnny) but his interest is dampened when Amsterdam discovers Jenny was once the Butcher's ward and still enjoys Bill's affections. Amsterdam gains Bill's confidence as Bill becomes his mentor. He becomes involved in the semi-criminal empire of William M. Tweed (Jim Broadbent) also known as "Boss" Tweed, a corrupt politician who heads Tammany Hall, the local political machine. Tweed's influence is spread throughout Lower Manhattan from boxing matches to sanitation services and fire control. As Tammany Hall and its opponents fight for control of the city, the political climate is boiling. Immigrants, mostly Irish, are enlisted into the Union Army as they depart the boats.

During a performance of Uncle Tom's Cabin, Amsterdam thwarts an assassination attempt that leaves the Butcher wounded. Amsterdam is tormented by the realization he acted more out of honest devotion to Bill than from his own plan of revenge. Both retire to a brothel, where Jenny nurses Bill. Amsterdam confronts Jenny over Bill and the two have a furious argument which dissolves into passionate lovemaking. Late that night, Amsterdam wakes to find Bill sitting by his bed in a rocking chair, draped in a tattered American flag. Bill speaks of the downfall of civilization and how he has maintained his power over the years through violence and the "spectacle of fearsome acts". He says Priest Vallon was the last enemy he ever fought who was worthy of real respect and the Priest once beat Bill soundly and then let him live in shame rather than kill him. Bill credits the incident with giving him strength of will and character to return and fight for his own authority. Bill implicitly admits he has come to look upon Amsterdam as the son he never had. The evening of the ceremony arrives. Johnny, who is in love with Jenny, reveals Amsterdam's true identity to Bill in a fit of jealousy and tells Bill of his plot to kill him. Bill baits Amsterdam with a knife-throwing act involving Jenny, where he targets her and throws the knife to leave a superficial cut on her throat. As Bill makes the customary toast, Amsterdam throws a knife at Bill, which Bill easily deflects and counters with a knife throw of his own, hitting Amsterdam in the abdomen. Bill then repeatedly beats and head butts him as the crowd cheers him on. The Butcher proclaims he will let Amsterdam live in shame (a fate worse than death) as "[a] freak. Worthy of Barnum's museum of wonders" before burning his cheek with a hot blade.

Jenny and Amsterdam go into hiding; Jenny takes care of Amsterdam and nurses him back to health. She implores him to join her in an escape to the frontier city of San Francisco. The two are visited by Walter "Monk" McGinn (Brendan Gleeson), a barber who worked as a mercenary for Priest Vallon in the Battle of the Five Points. McGinn gives Amsterdam a straight razor that belonged to his father. Amsterdam announces his return by placing a dead rabbit on a fence in Paradise Square. The rabbit finds its way to Bill, who sends Happy Jack to find out who sent the message. Jack tracks down Amsterdam and chases him through the catacombs into the local church where Amsterdam ambushes and strangles him. He hangs his body in Paradise Square for all to see. In retaliation, Bill has Johnny beaten nearly to death and run through with an iron pike, leaving it to Amsterdam to end his suffering. Mcgloin (Gary Lewis), one of Bill's friends, later goes to pray at the Catholic Church. Amsterdam had previously recognized him as a man who had fought for the Dead Rabbits years ago. When Mcgloin, a well-known racist, sees Amsterdam's black friend, Jimmy Spoils (Larry Gilliard Jr.), he objects to the idea of letting a negro in the church. Amsterdam and his friends respond by beating Mcgloin and the Archbishop joins in. The Natives soon march to the Catholic Church as the Irish, along with the Archbishop, stand on the steps in defense. Bill promises to return when they are ready and the incident garners newspaper coverage. Boss Tweed approaches Amsterdam with a plan to defeat Bill and his influence, hoping to cash in on the publicity: Tweed will back the candidacy of Monk McGinn for sheriff in return for the support of the Irish vote. On election day, Bill and Amsterdam force people to vote, some of them several times and the result is Monk winning by more votes than there are voters. Humiliated, Bill confronts Monk who fails to respond to the violent challenge, suggesting they discuss the matter democratically. Whereupon Bill throws a meat cleaver into Monk's back before finishing him off with his own shillelagh. During Monk's subsequent funeral, Amsterdam issues a traditional challenge to fight, which Bill accepts.

The New York Draft Riots break out just as the gangs are preparing to fight. Many people of the city, particularly upper-class citizens and African-Americans, are attacked by those protesting the Enrollment Act of 1863. Union Army soldiers march through the city streets trying to control the rioters. For Bill and Amsterdam, what matters is settling their own scores. As the rival gangs meet in Paradise Square, they are interrupted by cannon fire from Union naval ships in the harbor firing directly into Paradise Square. Many are killed by the cannons, as an enormous cloud of dust and debris covers the area. The destruction is followed by a wave of Union soldiers, who wipe out many of the gang members, including McGloin. Abandoning their gangs, Amsterdam and Bill exchange blows in the haze, then are thrown to the ground by another cannon blast. When the smoke clears, Bill discovers he has been stabbed in the abdomen by a piece of shrapnel. He declares, "Thank God, I die a true American." Amsterdam draws a knife from his boot and stabs Bill who dies with his hand locked in Amsterdam's.

The dead are collected for burial; Bill's body is buried on a hilltop cemetery, in Brooklyn, in view of the Manhattan skyline, adjacent to the grave of Priest Vallon. Jenny and Amsterdam visit, as Amsterdam buries his father's razor. Both decide to leave New York on a ship bound for San Francisco to start a new life together. Amsterdam narrates that New York would be rebuilt as if "we were never here". The scene then shifts over the next hundred years, giving a view as modern New York is built up from the Brooklyn Bridge to the World Trade Center, and the graves of Bill and Priest are gradually forgotten, being overgrown by bushes and weeds.

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