I'm not sure if this counts as "HiE". A human's mind is imprisoned in Celestia's consciousness...and the human is the bad guy.

In this story, our unsuspecting narrator, a simple human teenager named only John Doe, finds that his entire consciousness has been transplanted into Celestia's mind. But rather than him becoming the ruler of Equestria, he's completely helpless; a prisoner in an alien body, only able to communicate with Celestia when she goes to sleep and her subconscious defenses are lowered. Will he eventually overcome her defenses and wreak havoc on Equestria? Only time will tell.