Mondo grew up on the dark side of the Moon with his brother David and a magical unicorn. For some reason involving dark moon energy, David later killed their mother and cut off Mondo's left arm, but the unicorn used its magic power to help Mondo escape. Mondo later appeared in the office of a State Executioner named Brian, having lost his memory. Brian saved him and replaced his missing arm with the Musselback, cut off from the target of a previously successful execution.
Some time later, Mondo found a lost girl named Mika Takizawa and the two of them joined the office of the State Executioner. Mondo performed several jobs for the State, but accidentally started catching up with his past when a woman named Moon River asked him to execute David, who had allegedly stolen the Moon from her eyes.
Mondo noted that he could breathe on the Moon without any need for a spacesuit, and found it odd, but continued on to face David. David knew about him already, and offered to rule the Earth with him, but Mondo refused and set to kill him. However, David escaped, saying that Mondo needed more blood to kill him.
Mondo then returned to his work, putting David's execution on hold while letting Moon River stay on his houseboat. After a few more jobs, Mondo slowly started remembering his own past in dream sequences, where a mysterious lady in red started stirring up long-buried memories shortly before Mondo was tasked with executing her, including the fact that David was a state Executioner who rescued Mika from a kidnapper long before Mondo ever got the position.
Upon realizing that David was his brother, Mondo decided to finish his execution anyway. Fighting his way through the Moon mansion again, he fought David in a final battle and cut off his head when he appeared in his old Executioner form.
At the end, Moon River came back to the State Executioner's office, asking them to execute the man in the photograph she held. While the target is never truly revealed, the scene switches to a man who appears to be Mondo brushing his hair while the broken mansion reconstructs itself.
Mondo only carries his beloved katana "Gekkou" and his mechanical left arm "Musselback" into battle, but these are the only tools he needs to do his job.
Throughout the game, Mondo's moves can be purchased and upgraded with golden "moon crystals." The Gekkou can be upgraded to perform an area of affect attack or a launcher, and it's power can be increased in proportion with the length of a combo. Though Musselback's standard cannon is the only required weapon, additional add-ons can be unlocked by successfully completing Gigolo Mode missions. The mechanical fist itself can be used to break through the guards of enemies and to continue combos.