IMHO the "documentation" consists in 3 major "categories":
- In-game help. There is one already, and it explains the basics, like how to build a base, of what discovery/suspition is. It can be improved tho, or made more visible. It does not dive in too many technical details since it could spoil part of the fun. Help sections are added to the list when player researches their associated technology or is able to build a given base/cpu/hardware, and this "on-demand" feature could be highlighted too.
- Game mechanics documentation, off-game: tech-tree and full data (suspicion rate of bases, tech costs, etc). This is needed, but would /surely/ ruin the fun for those who haven't played till the end for the first time. ("wow, you can build a base on the xxxx!! COOL!"). These are easily read in game's data files, which are text files. Maybe we can create a "Database" button for players that have won the game once.
- In-game tutorial: the one I would love the most. The AI would guide you on the first steps, so you get a glimpse of what the gameplay is about. I've seen many newcomers ask: "ok, what am I supposed to do? What is the goal?". They must be oriented that the game is about building bases to get more resources, use some of those resources to avoid being caught, and use the rest in research, which is, fundamentally, the main goal ("I must study")