The third stage is a Breather Episode, allowing your characters to heal nearly all damage but likely inflicting blight, symbolizing how your hamlet is, at the moment, a safe haven.The Ancestor avatar itself is the 'easy path', such as the destruction of the low-health psychological-damaging enemies over the more robust, physically stronger foes, or just the destruction of monsters over solving the long-term issues of the Hamlet beyond monsters, including the abundance of disease and the Hamlet's isolation. In other words, metaphorically speaking, the abyssal pits are the strange things going on in the world you (the heir) never attempt to fix, such as the corruption in the Weald. The three abyssal pits of darkness represent everything you can't easily defeat or understand.

The second stage involves a tug-of-war between your characters and the Ancestor avatar and the abyssal pits of darkness allied with him.

This fight represents your willingness to murder anything and anyone in your way and butcher that which is outright disgusting, all to deal Scratch Damage to the final boss.

The first stage involves defeating clones of the Ancestor, where each kill of a mutated clone will damage the otherwise invincible boss.

Specifically, the final boss is a general metaphor for the damage you (the heir) have done to both foe and ally alike to get this far.

The final boss is mocking you and your struggle.

Since said monsters are nothing but incomplete skeletons of swordsmen totally embedded in a huge mass of goo, it wouldn't contain anything useful, as any item the heroes could theoretically find after searching through the remains would be too filthy or too damaged to be valuable anymore. Battles against Ectoplasms and/or Large Ectoplasms (only when they are the only monsters involved in the fight) don't grant any loot at all.

Darkest dungeon all ancestor quotes