“Johnny Mnemonic” is set in an ultra-high-tech, near-future metropolis in which data is closely guarded by both legal and criminal organizations. The protagonist, Johnny, is a data trafficker whose job is essentially to be an information mule. Clients store information within him by cybernetically placing him into a hypnotic state. He delivers the information to the recipient, securely and without knowing what the data is about.

Johnny goes to a bar in search of a client, Ralfi Face. Ralfi owes Johnny money and has sent a hit man after him, so Johnny still has not delivered the data to him. Johnny finds Ralfi and his imposing bodyguard in a bar. As Ralfi and Johnny begin to discuss the disputed transaction, the bodyguard stuns Johnny with a “neural disruptor.” Ralfi tells him that the data was stolen from the Japanese crime organization known as the Yakuza.

At that moment, a cyborg named Molly Millions walks to their table. She offers to sell Ralfi “some good free base” (5), but when the bodyguard moves to attack, she cuts his wrists using razorblades embedded in her fingertips. She also takes the stun device and unfreezes Johnny. Ralfi offers to pay her off, but Johnny instead hires her as his own bodyguard. They take Ralfi hostage, but just as they exit the bar, a Yakuza assassin slices him into pieces with a monomolecular wire hidden in his thumb.

Molly and Johnny escape. Johnny is determined to extract the data from himself to avoid being assassinated. Because the data is encrypted, however, that task is almost impossible. The only method involves hiring a Squid—a “superconducting quantum interference detector” (10)—who can uncover the password protecting the data. Molly knows a squid, a cybernetic dolphin who formerly worked for the navy. The navy caused the dolphin to become addicted to heroin, so Johnny trades drugs for the password.

After putting Johnny in a trance, they retrieve the stored information, which Johnny thinks is “probably research data, the Yakuza being given to advanced forms of industrial espionage” (18). They attempt reverse blackmail to get money, though it means putting Johnny’s life in continued danger. For safety, Molly takes Johnny to a marginalized area high up in the city where a technology-opposed fringe group known as the Lo Teks live. They realize that the assassin is following them, so they lure him to an area known as the Killing Floor.

Molly and the assassin fight on the arena-style Killing Floor before a crowd of cheering Lo Teks. Through some elegant dance-like moves, Molly tricks the assassin into cutting off his own hand. Mortally wounded, the assassin leaps down from the Lo Teks’ domain. Johnny and Molly stay among the Lo Teks afterward, creating a new business using the Squid to retrieve data from former trafficking jobs, which Johnny then uses to blackmail his ex-clients.