Erebus is the collective human thoughts of death and despair. Erebus making contact with Nyx resulted in The Fall, which could bring about the end of all life. In Persona 3: The Answer, S.E.E.S. learns the protagonist used his life's essence to create the Great Seal, preventing Erebus from contacting Nyx and continuing The Fall.
Although S.E.E.S. defeats Nyx, they realize Erebus cannot truly be destroyed until the heart of every person stops wishing for death. Together, they vow to keep moving forward and hopefully change the world someday to make the protagonist's burden less heavy.