Three years have passed since Travis Touchdown became the top assassin in the United Assassins Association (UAA) and walked away. He has returned to Santa Destroy and fights Skelter Helter, who seeks revenge on Travis for killing his older brother Helter Skelter prior to the first game. After winning the battle, he meets Sylvia Christel, who informs him he is ranked as the 51st best assassin. The nearly-dead Skelter Helter interrupts them and warns Travis that he and his co-conspirators will still have their revenge.
There are four beam katanas, which Travis can freely switch between in the middle of battle, each with different properties. For example, the Peony is a large and heavy sword with a wide range, and the Rose Nasty consists of two beam katanas which Travis dual-wields. There are two sections in which Shinobu and Henry are playable, both of whom have different capabilities from Travis. Shinobu can jump, and her section contains some platforming elements, while Henry has the ability of making a quick dash in all directions by using the B button on the Wii-remote.