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.