How does one go about modding a game?

I know it’s obviously different depending on what game you are wanting to mod. The game in general that I want to mod is called Endless Space, more info about the game can be found here —It’s essentially a 4X game (Explore, Expand, Exploit, Exterminate) similar to the Civilization games, but this one is based in space.

The Goal is to take this Endless Space game engine and mod it so that it plays like a 4X Star Trek game (similar to Birth of the Federation for those who know of that game), so instead of the Endless Space races/factions and their ships, you would choose from the races and factions from the Star Trek series.

Has any Flutherans out there ever modded a game? If so, are there any links or tools that make it easier to accomplish? As I’ve never modded a game, there may be other questions that I’m not even asking. Seeking the help of those with this kind of experience! :)

Edit: How is Star Trek NOT a Fluther category?!