From level 6 onwards players will be able to build an armoury – this will give access to particular improvements to certain units via “equipment”. To unlock and then upgrade the equipment you will need to collect a certain amount of “fragment data” obtainable via supply crates. The upgrading will be in the existing research lab, and you cannot upgrade anything else while upgrading equipment.
As an added twist, the equipment may in some circumstances only be used on certain planets. Other than that, it is up to you what equipment to activate and deactive.