Zenos is... [big fat spoily]
...still alive.
We thought he was dead when he merked himself in Ala Mhigo, but we learned that, similarly to that one fish man who turned into aether and possessed another one of his kind after being shot by Tall Trenchcoat Lady, he was able to do the same with a Garlean soldier in order to reclaim his body.
Who's to say that he didn't do the same with a random Loporrit onboard the Ragnarok... or worse, the Warrior of Light?
We did do that creepy smirk thing back to him during the final battle. I think he already wormed his way into our head, made us susceptible to be used as a vessel to carry him back to Hydaelyn (the planet, not the god).
Get ready for Zenos for three more expansions!