Throughout your playthrough(s), you will come across cylindrical chests that have loot in them. They'll either be a weapon, ability, or enhancement. Each floor has a specific number of loot and you can check your overall progress on the big overseer board next to the chair you enter. Once you have unlocked something, you'll be able to purchase it for your next agent in the area above the chair.
You will unlock almost everything simply from finding these upgrade chests in the normal and special levels, but there are 8
gold chests which only appear select special levels (you enter a special level by going into a purple elevator instead of the green (exit) one).
Because each route to the Overseer is randomly generated for every new asset your choose, there is not a way to choose the special levels with gold chests in them. I recommend checking a guide against the names of the special levels you enter (or remembering it), that way when you actually get the special level with the gold chest, you won't miss it!
Hooloovoo has a great guide on the steam community site complete with annotated screenshots for the secret weapons, abilities, and enhancement which you can find here
https://steamcommunity.com/sharedfiles/filedetails/?id=68153... and I recommend you read it.
The special levels you need to watch for are:
* Fireworks (1st floor)
* Locked Out (2nd floor)
* Triple Towers (2nd or 3rd floor)
* Exordium Imports Inc. (3rd floor)
* Hovertank boss fight (3rd floor)
* Welcome Back? (4th floor)
* Commuter District (4th floor)
* Emergency Accomodation (5th floor)
For the Fireworks and Commuter District special levels, you will need a
rocket or
missile ability (or rocket launcher) and for Exordium Imports Inc. you will need an
explosive ability or weapon. I unfortunately found the Fireworks level, but had a grenade launcher ability and I wasn't able to shoot across the gap to destroy things I needed to.