From version 1.3.2 modding the game should be easier. For this, I've set up a GitHub project that contains a stripped-down Unity project that we use ourselves to build the full game.

GitHub repo https://github.com/tlaasik/stte-mod/

It contains some complete assets that can be edited and exported into asset bundles that the game can load. This way it is possible to add or modify ships, modules, crew, levels, POIs, shops, projectiles and more.

Since the game is big and complex, items in the game often pack a lot of detail and without some help from us it's probably hard to create or change those items. Therefore it would be really helpful if you post questions here about what you want to mod and then we can write up wiki pages about it.