In early 2004 the source code for the game logic was released in an SDK, enabling a number of mods to be created. Previous modifications, such as the popular ET Pro competition mod, couldn't change much. The source code allows more flexibility for mod makers. The game engine remains closed source as of 2006, but the source code to Quake III Arena was released in August 2005.

The Quake 3 total conversion mods Enemy Territory Fortress (ETF for short, formerly Q3F) and TrueCombat (known as TrueCombat: Elite in its ET incarnation) have been ported to Enemy Territory. Other mods, which consist of little additions and fixes to the game mechanics rather than a total conversion, include ET Pro (used in competitions but also popular in public play), ETPub, Jaymod, No Quarter, and Wolfenstein: The Frontline (although the current release still has the original name of FalckonET)