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Officially there is no canonical ending, both endings did happen.
Cate and Michael both dead in the end of Heroes 6.
But we would like to think that the Tears ending
is the most canonical one in the sense that the Hall of Memories were destroyed,
the souls of the dead Angels killed
during the Elder Wars have been liberated and so the cycle of hate was broken.
Michael did lead the troops of Haven against the Faceless in the Abyss as seen in the Blood map.
When the Hall of Memories was attacked he was forced to come back.
It is how he appears at the end of the map.