Great story! Mind-controlling aliens, VR rebellions, autistic heroes. I'd love to see a sequel!
This one carries on in the theme oft-used by Stephen King where those characters who have different mental conditions always have some extra power above the rest of us (see Dreamcatcher, Rose Red, Kingdom Hospital, The Regulators, etc...).
The POV of a mind-controlled human was very interesting, and I loved that the humans are just virtual grunt-labor. Imagine how much damage that guy could've done if he had collaborated with someone else, someone who could've barricaded the door, or able to disable attackers!