Asano, an investigator for Japan's security police, visits Logan in New York. He explains that the father of Logan's former girlfriend, Mariko Yashida, is arranging a political marriage for her. Her father, Shingen Yashida, is the leader of the organized crime organization, Kuzuryu, and this marriage will solidify his power in the region. Logan travels to Japan and invades Shingen's residence, finally reuniting with Mariko. But the reunion is short lived when he meets Mariko's betrothed, Hideki Kurohagi, and her father, Shingen.
Having fallen into Shingen's trap Logan ends up in dire straits, but is rescued by a mysterious woman known as Yukio. Later Logan visits Asano's safe house and discovers the dead body of Asano. Suspected of his friend's murder, Logan is pursued by the police.
Kikyo Mikage, a mutant assassin of Shingen's who has adamantium weapons, attacks Logan who's fleeing the police. Escaping, he and Yukio track down Kurohagi's secret smuggling operation. But... when Logan arrives at the harbor, his arch-enemy Omega Red appears.
The battle between Omega Red and Logan continues, while Asano's squad discovers that Logan isn't responsible for his death. Scoring a narrow victory , Logan heads to Shingen's, where he finds Kikyo waiting for him. Omega Red, who has since recovered, also arrives, leaving Logan caught between a rock and a hard place .
Logan finally manages to defeat Omega Red, and he and Yukio fly off to the crime ridden city-state of Madripoor, where Mariko is to be married. Things get off to a bad start with the locals, and Yukio and Logan get split up. Logan narrowly escapes with help from a young street girl named Min, who is part of a resistance army that lives in the tunnels underneath Madripoor.
Kurohagi gets A.I.M. to help him send Vadhaka, the guardian statue of Madripoor, after Logan as an assassin. Logan manages to overcome the attack, while Min leads them to an underground town, where they meet Koh, the leader of the resistance group.
Logan and Yukio start down Hell Road on their way to the Dragon Palace, where Kurohagi and Mariko are to be married. Somehow the two manage to overcome the many traps that have been set along the road, while Koh and his army follow, intent on attacking the Dragon Palace himself.
Having managed to fight their way through Hell Road, the statue of Vadhaka once again appears before them. Meanwhile, the preparations for Kurohagi's marriage to Mariko are progressing inside and Kikyo watches on the sidelines while Logan and Vadhaka engage in a fierce battle.
Logan manages to enter the Dragon Palace, with Yukio and Koh following him in, each consumed with their own dark thoughts of revenge. Waiting for them inside are the deadly sword skills of Shingen. Kurohagi and Mariko's wedding is about to start, does Logan have any hope of stopping it in time?
Logan engages in his final battle with Shingen inside the Dragon Palace. At the same time, Yukio is heading toward her own final battle, while Kurohagi makes a last ditch attempt to make Mariko his own. It's all come down to this, how can Logan save the love of his life?