Black Samurai opens in March 1973 in Tokyo, Japan. Leo Tolstoy, a disgraced former US Army colonel, raids three buildings that house a samurai master and his students. Among them is Robert Sand, aka The Black Samurai, a Black American former GI who has been living with Master Konuma and his samurai brothers since 1966, when Sand intervened against other GIs who were harassing Konuma on the street. Tolstoy has just kidnapped Konuma's granddaughter, Toki Jakata Bi, as part of a plan to massacre an American town, doing to it what he did to a village in Vietnam; he knows he must kill Konuma and the Black Samurai because they will hunt him down otherwise.
Sand is the only samurai to survive the raid, which ends with Konuma dying in his arms. He resolves to avenge his master's death and kill Tolstoy. Sand leaves the burning houses on foot, then rides a golden mare into Tokyo, where he meets with former US President William Baron Clarke. Clarke knows through his network of contacts that Tolstoy is planning an attack with his band of international terrorists and will try to kidnap his daughter Mary Clarke as well. Olden reveals that Clarke has been employing Sand as an assassin for several years; their targets are men who pose a threat to the world. They have been monitoring Tolstoy. Clarke uses his influence and money to arrange for Sand to travel to Saigon on a fake passport, where they expect he'll encounter Tolstoy's men.
In Saigon, Sand relies on Clarke's contacts to set up a sneak attack on Long Minh Sat, a Vietnamese war criminal who Tolstoy has sent to Sand's hotel to kill him. Sand then travels to the villa where he believes Tolstoy is holding Toki. Sand sees Toki in the window of the villa. To intimidate the men waiting inside, he cuts off the head of an opponent and tosses it in the window. Two of the fighters defect from the mission, killing their higher-up and fleeing as Sand watches. Sand then battles two Korean contract killers in hand-to-hand combat as they hold Toki captive. Sand kills both men only to discover that the woman he believed was Toki is a decoy, and is now dead. He is relieved to know Toki is still alive somewhere. In a flashback, Olden reveals that Sand is in love with Toki, who reciprocated his interest long before she married a Vietnamese official.
Meanwhile, Tolstoy goes to Paris to meet with Coleman Near, an illegal arms dealer who is secretly in touch with Sand and Clarke. Tolstoy employs James Devlin Winters, an IRA member, to kidnap Mary Clarke while she is on vacation in the city. Sand flies to Paris in time to thwart the kidnapping and kill Winters. Once Mary is safe, Sand goes to the barn full of munitions needed for the massacre; Near has led Tolstoy and his men there. Near dies from a grenade attack while Tolstoy and several of his men escape in trucks.
While Tolstoy travels to a hidden airfield in Canada, near to the American town he plans to massacre, Sand's next stop is New York City. St. Paul Braeden arrives in a helicopter to kidnap the wife of a Chinese ambassador—the third hostage the group has planned to take. Sand and a Secret Service member named Frank Pines are ready for Braeden and his fighters, all of whom they kill or take into custody.
Sand makes the helicopter pilot bring him to the airfield in Canada. Upon arriving, Sand attacks Tolstoy and his remaining men from the shadows. Clarke and Pines soon arrive in another helicopter to help Sand take down Tolstoy. The book reaches its climax when Sand rescues Toki from Tolstoy and throws his short samurai sword at Tolstoy's throat, killing him. Sand tells Toki he loves her for the first time.
The novel ends several days later as Toki flies back to her husband from New York. Sand gets in a car with Clarke and Pines, explaining to them that he should have told he loved her years earlier. She is now committed to an honorable man.
