Jones began programming on Apple computers in high school, assembling a multiplayer game called Minotaur: The Labyrinths of Crete.

Minotaur: The Labyrinths of Crete shipped in April 1992;[3] while the game sold only around 2,500 copies (it required a then-rare modem for network play),[4] it developed a devoted following.

Since Bungie had no money and Jones was the only one with the available time, he single-handedly coded the game on a Macintosh IIfx, passing art chores to his friend Colin Brent.

The game included state-of-the-art graphics, network multiplayer, and voice support, and won a number of awards on release in 1994.

[4] Jones recalled that he was surprised anyone ever completed the game and sought to atone for some of its shortcomings with its sequel, Marathon 2: Durandal,[7] which was also released for Microsoft Windows.

Jones recalled that the buyout was a "blur [...] We'd been talking to people for years and years—before we even published Marathon, Activision made a serious offer [to buy us].

"[10] Around the same time, a glitch in versions of Myth II was found to entirely erase a player's hard drive; this led to a massive recall of the games right before they shipped, costing Bungie nearly one million dollars.

[13] Jones led the development team that created its sequel, Halo 2,[14] and served as director on a new video game series, Destiny.

[21] As development continued, and with Griesemer gone, the writing team led by Joseph Staten had created a "Super-Cut" which was essentially a summary of the game's story-line.

[21] Shortly after, Jones decided to scrap the writing team's work and effectively re-write the story very late into production with Marty O'Donnell, believing it was not feasible and almost impossible to complete.

[21] Knowing the game was in peril with his proposed reboot of the story, Jones formed a group called the "Iron Bar" composed of art director Christopher Barrett, designer Luke Smith and writer Eric Raab, an experienced book editor.