Mods are modifications to the base game, ranging from balance changes and additions of content to full rehauls and tools to help other people modify the game. Mods are generally made for Update 19, Update 98, or Nuclear Throne Together (NTT).
Nuclear Throne Together Edit
"Nuclear Throne Together is an experimental mod for Vlambeer's Nuclear Throne, improving the multiplayer-related aspects of the game, adding modding support, and, most notably, adding online multiplayer support for 2-4 players."
Nuclear Throne Together adds mod support for online and offline play. While modders may not have complete, direct access to the source code of the game, they can still complete very complex tasks in terms of modification for the game such as new races, areas, enemies, weapons, and more. NTT also runs on a modified version of Update 98, so the game content is very current and even includes fixes to bugs that are present in vanilla Update 98.
Update 19 Mods Edit
Update 19 mods are made for a much simpler version of the game but they are generally made by altering the source code, giving a wide range of what one can manipulate in the game. Most Update 19 mods can be found on Thronebutt, though some may also be found on itch.io.
Update 98 Mods Edit
Aside from earlier versions of Nuclear Throne Together, there are not many mods for Update 98 that go past modifying in-game sprites, as Update 19 was the last version of the game to run on GameMaker 8.1 which allowed file manipulation. One depository of Update 98 Mods is located here. There is also a seeding tool for Update 98 that can be found here.
Custom Throne Edit
Custom Throne is a "modding toolset that lets you create levels, weapons, characters, enemies, mutations and more, running on a heavily updated u19 engine." It allows for modification of an updated version of Update 19. A depository of Custom Throne mods can be found here.