Johnny Mnemonic is based on William Gibson's short story and a subsequent movie of the same name. The game's plot bears more similarities to the movie than to the original story. Johnny is a courier in a futuristic society, delivering data implanted in his brain. However, the latest delivery is so big that it can kill him if he doesn't download the data. Unfortunately, the only person who knew the password is dead, and members of the Yakuza are hunting for the data and for its living container.

The game takes place in the near-anarchic future of the year 2097, in which the world's economy has been devastated, governments have collapsed, and organized crime has gained dramatic influence. In X-Kaliber 2097, the player guides a swordsman named Slash through a side-scrolling environment. Boss encounters take place as one-on-one matches in the style of versus fighting games.