Humanity has already fought its war against the machines -- and lost. AI death squads stand watch over every planet and every wormhole, the few remaining human settlements are held captive in orbiting bubbles, and the AIs have turned their attention outward, away from the galaxy, to alien threats or opportunities unknown.
This inattention is our only hope: a small resistance, too insignificant even to be noticed by the AI central command, has survived. These are the forces you will command. The AI subcommanders will fight you to the death when they see you -- but your glimmer of opportunity comes from quietly subduing those subcommanders without alerting central processing to the danger until it's too late. You do have a few things going in your favor. Your ships are much faster. You have safe AI routines to automate defenses and mining outposts. You have production techniques that can churn out fully-outfitted unmanned fighters in seconds. There will never be more than a few thousand of your ships versus tens of thousands of theirs, but through careful strategy you must somehow reach and destroy the heavily-guarded AI cores. Go forth into the galaxy, steal AI technology, recapture those planets you must in order to achieve your ends, and save what remains of humanity. But draw too much attention to yourself, and the full might of the AI overlords will come crashing down. The only way to play is in procedurally-generated "campaigns." There are quite literally billions of possibilities, and every campaign has a really different feel to it. They also last a good while: most between 7 to 13 hours, about the length of time it takes to play through an FPS campaign once. This means your decisions -- victories and blunders alike -- have really long-term, interesting consequences. Some players talk about feeling bittersweet when they conclude a long campaign. You can save and load at any time, even in multiplayer, so you could have one campaign going for weeks or months if you like.