Main progression system:
This is the factory you build between pauses. It produces resources that can be used to fight. To progress in the wave fighting. You can craft items and buildings or use assemblers to let them do the work.

Secondary:
This is the level up mechanic. With each level up you unlock a new building that is useful in the factory world. In addition each level up gives you the opportunity to continue building your factory

Jam Version:
The turret is broken here.
Sorry for this. Please play V1.1 for a working turret.