Personally, I don't think that it was Zodiark. Why would he feel the need to talk with anyone other than the WoL? Or with the Echo, even? No, whoever it was, it targeted the Scions specifically (which also rules out that Zodiark can't control how he talks to us, because in that case someone out of the Scions would've heard him too).

My first thought was that maybe it was Minfilia, that she saw or knew something and decided to contact her old friends to avoid it. The fact that Thancred was the first to "leave" reinforced my theory, as I thought that being more sensitive to such aether stuff due to the ascian possession maybe he noticed that it was her and he wanted to stay wherever she summoned us. Of course, the voice was a male, but wouldn't it be too obvoius then if we had heard a clear female voice, or directly Minfilia's?

However, I think that Fleurette's theory has more sense in that regard, and covers what I mentioned on the first paragraph. But I don't think that Alphy will get possesed or anything. Remember who he's descending from: Louisoix, who coincidentally was able to send us to the future after Bahamut came out of Dalamud. I'm quite sure that good old Alphy would be able to at least contact us in the past somehow, to prevent whatever is about to happen if we keep doing what we are doing.

Now, about that, I think that the solution will be that the WoL will also become the WoD at once. Neither light or darkness are bad per se, so if there would be a way to make them find a balance wihout having to go the Calamity route, I think that our favourite herowould be the one to start it. We don't know how far in the future would we face the bad consequences of our current actions, so maybe a "small" change like the WoL representing both light and darkness too would change everything over time. That way we can get rid of the ascians, while preventing a flood of light.