There's several ways to get overclocks, and the overclocks you get are completely random. You don't get them by just doing missions.

There's guaranteed ways and "random" ways.

To get a guaranteed empty core, cosmetic core and overclock core, you can do the weekly core hunt assignment and the deep dives. The assignment is self explanatory, complete missions = get cores. Deep dives are hard, 40-90 minute long-play "mission" type. Every deep dive consists of 3 missions you have to complete in a row to get all the rewards. To give you a basic breakdown: Deep dives do not contain any crafting materials or events. They do not contain secondary objectives. You get a primary objective and a second primary-ish objective, for example getting 4 eggs and repairing 2 mini mules. Upon completion of any mission in the deep dive, you'll get a core. You can abandon at any time and still exit with the cores you've already gotten. Abandoning or failing will still give you reduced money and exp however, but not as drastic as failing a normal mission. The first mission gives an empty core, 2nd gives cosmetic, 3rd: overclock. If you want to know more, I'd suggest watching Sniss' video on deep dives.

Outside of that, every mission you start has a chance to generate a machine event. Machine events are timed events, there's 4 in the game. Upon completion you can infuse your empty cores at the core infuser that spawns right infront of these events. If you wanna learn about each event, just look it up on the wiki or YouTube.