You get them by playing, either as drops (like score drops) or by completing side objectives, which change every playthrough.
You can earn I think up to 50 total ops points in a single run, 40 from side objectives and 10 from pickups. The more ops points you have, the tougher the enemies will be.
Each run you do you start with an increase of 5 ops points, so the first playthrough you start off with 5, second playthrough you start with 10, third with 15, fourth with 20, etc.
Resetting your ops points will make the level easier, but you will lose any rewards you get from having an amount of points at the end of the level (40 for a skin, I think 60 for a commander pack, and theres more further on).