Combinations is opened by revealing blueprints. So laser cannon T1 can be nanolathed (combined) to T2, and then to T3.
Energy generator can support tower with faster recharge rate. But when nanolathing - it convert laser tower to gatling laser, cannon - to minigun, missile launcher to fast SRM.
Blueprints can be opened at end of level or droped from enemies.
Loot gathered from enemies provide upgrades for ship and modules.
More powerful ships gain access to big guns. But with cost - they can be combined with dominoes/triminoes/tetrominoes to work properly. I.e. giant laser cannon (4x4) must be combined from 8 lasers, 4 generators and 4 accumulators.