This is a complicated question becuase It depends on what you mean by mystery. Not every unanswered question is likely to be answered. For instance: it’s unlikely that after 20 years we are going to find out where the Dwarven Gate on Ulgrotha went.
So, keeping in mind Mysteries that Vorthos today would care about and are likely to have an answer:
– Bolas’s End Game
– The identity of the Raven Man (http://www.mtgsalvation.com/articles/49659-who-is-the-raven-man)
– The Heliud/Heliod relationship (http://www.gatheringmagic.com/carythomasbarkett-06032016-breaking-down-the-order-of-heliud-and-heliod/)
– Why did Emrakul seal herself into the moon?
I’ve heard a theory on Emrakul. It goes like this:
– Role of the Eldrazi titans is to fit in a “life cycle” of a plane. At a point when a plane has too much mana ,it may become unstable (zendikar and roil)
-Ulamog eats, Kozilek digests and Emrakul turns the digested mana into a new thing.
– When Emrakul suddenly appeard on Innistrad, she did what she was pre-programmed to do – create, which resulted in horrible mutations.
– She saw, that she shouldn’t be doing this, so she locked herself up in the moon.
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