You, with the help of the Underground, a covert resistance movement who never get organized enough themselves to put information together and stop the oppression, can overthrow the Tzorgs. I have asterisked out quests where you just need to find information. They are not strictly necessary, but they are neat puzzles. They may require knowledge found elsewhere in the game. If you really need to improve affinity just talk to someone, cut off the conversation, and talk again.
Agility comes from fixing or using weapons, and intelligence comes from fixing or using items.
You can pretty much futz with a teleporter or a gridread or a scanner and get intelligence to 99. They're not worth it. Boost labs are too hard to get to if you want an efficient walkthrough, although they are a neat puzzle. Look for Fritz in the underground if you really want to know. The first thing to do is to go to Joe's Bar.