Red Sky takes place in a version of Earth where the most prevalent threat to society was a bioterrorist scare during Y2K. Because of this, the Eden project was put into place; a lab network called Genesis Labs began production on a series of near-microscopic android life forms, which would attach themselves to humans harmlessly, feeding off of their blood to stay functional as well as removing the harmful components in a person's blood, and using electromagnetic fields to stay on their hosts.
However, the bioterroristic threat never came to fruition, and Y2K came and went with no changes to daily life. The Eden project was abandoned, but a subset of Genesis Labs, called the Tree of the Knowledge of Good and Evil, continued work in secret. Feeling bad for the Nanites' autonomous lives, in which they were created to serve humans but not to have meaningful experiences of their own, TKGE gave the Nanites the ability to be conscious of themselves and to become independent beings.
Unfortunately, this act of kindness was taken advantage of. The Nanites used their comrades in the TKGE to begin mind-control of humanity, and forty years later, Nanite-controlled humans make up a majority of the population. Because of their ability to pass themselves off as completely human, as their malevolence lies in controlling the body of their human host, most free humans are completely unaware of the fact that they are often surrounded by Nanite-controlled counterparts.
Red Sky focuses on Jordan Foster, a senior in highschool, scheduled to be taken over by his Nanite, Mason Skino XII v1, at the end of graduation; though when that doesn't happen, and Jordan and Mason become friends and eventually lovers instead, they realize that they may be some of the last free people in this world.