It's stated at the end of the game that the Foxo that chases you is merely a fake and that the real Foxo (along with everyone else in Power of Friendship as implied in that mode's ending) was being held captive by the Principal. My theory regarding the lore is that the Principal created the clone of Foxo (along with the other distorted Foxos that appear in Wrath and STOP mode) to serve as a facade to cover his corruption of the game. As for his motives for taking over? No idea, which is why I agree that we should get a more comprehensive story this time around.