As you go through the game, watch for people with yellow bubbles over their heads. When you speak to these people, you will receive "recipes" for factory blueprints. Sometimes, you'll have to speak to two different people to get the whole recipe. Once you complete Chapter Five (the hacker in the factory), the factory will become available for your use. I've written description on how to use the factory
here.
If you're missing any blueprints, you can find locations
here. I take no credit for the faq.