Season 6 dealt with the aftermath of the Apocalypse. Sam returned from Hell without his soul, Castiel waged a secret civil war in Heaven, and the "Mother of All Monsters" — Eve — was introduced as the progenitor of every monster species.
Creatures Introduced
The Alpha creatures (the first of each monster species) were introduced. Skinwalkers, fairies, the Khan worm (a parasitic creature), the Phoenix (from the Old West, killed by Colt ashes), and Eve herself all appeared. Djinn variants (fear-feeding subspecies) expanded on previously established lore. The concept of Purgatory as a real, accessible location was established.
Major Lore Developments
The Mother of All (Eve) was established as the creator of monsters, with all monster species tracing back to her. Her defeat required Phoenix ash — a substance obtained through time travel to the Old West. Castiel's arc — secretly working with Crowley to open Purgatory and absorb its souls for power — set up the Season 7 conflict. Sam's soulless state explored what a person becomes without conscience, empathy, or moral restraint.