The player takes on the role of Moss, a hacker who breaks into computer systems in order to afford a $700/day drug to slow the progress of his phage affliction.

Using programmable software agents called EXAs, the player must accomplish each given task by writing computer code to cleverly manipulate the data stored on the network's systems.

Typical missions include retrieving data from secured storage systems, hacking into company databases, and causing an automated teller machine to dispense free cash.

Some puzzles challenge the player to hacker battles, where they must pit their EXAs against an opponent's agents, for example altering a television station's program to broadcast Moss' content instead.

Zach Barth, the founder of Zachtronics, was inspired to create Exapunks after reading about the Stuxnet viruses that had impacted a nuclear facility in Iran in 2010.

[2] He developed Exapunks's lore on the cyberspace culture envisioned by William Gibson, though with more focus on the "punk" side of the 1980s and 1990s - small-time hackers fighting against large corporations.

He also took inspiration from 2600: The Hacker Quarterly and attended various DEF CON events, while the game's writer, Matthew Burns, also considered cyberculture works like Wired, Transmetropolitan and Tom Clancy's Net Force Explorers influential.