Everything else encountered so far, including the Thing, Sleeper, and the Spreading Stain are ultimately just agents, proxies, or manifestations of it. It's also revealed that the Iron Crown itself is the ultimate evil and villain of the entire setting.

This causes them to break the barriers between realities and unleash the Spreading Stain, dooming reality and causing the apocalypse. This eventually culminates in the Protégé performing their own version of the Iron Crown ritual that the Ancestor tried to use them for with them using the Academic as the final sacrifice.

The now mentally-destroyed Protégé became obsessed with the Iron Crown snd began falling into more and more depraved research regarding it, either the Academic desperately trying to stop them. It's implied that them telling the Ancestor about their research is what ultimately helped convince him to unearth the Darkest Dungeon beneath the Estste in 1 and rouse the Thing. Act 3 reveals that the Academic and Protégé got invited to some party hosted by the Ancestor where they told him about their research into the Iron Crown, did some messed up rituals with other occultists, which eventually led to them discovering that the Ancestor intended to kill everyone there (the Academic rightly told the Protégé to barricade their door during the night) and perform a depraved ritual to invoke the Iron Crown that mindbroke the Protégé and forced the Academic to take the both of them and leave as fast as possible. The new guy is the Academic, who was the Protege's (your player character) friend and mentor before awful shit went down and the world went to hell.

Flagellant skills darkest dungeon