Ok, wait a second here, <Puts on Darksteelfoil Hat> Alright, Midgardsormr made some kind of pact with Hydaelyn in the Time before Time, He was charged with aiding "Hydaelyn's Chosen One" (The MC WoL) and to guard some kind of seal in Silver Tear Lake.

Ok, from 1.0 we know Midgardsormr made contact with The Twelve during The Divine Era not long after the Creation of Silver Tear Lake. We also know there is some kind of Crystal Under Silver Tear Lake. The Agrius exploding weakened the Seal of Silver Tear Lake enough to unleash large amounts of aether and destabilizing the aetheric flow in Mor Dohna even further and making it possible to summon The Primals (Again?).

So lets say Zodiark WAS sealed by The Gods (Hydaelyn and The Twelve in this case) WHERE was he sealed?

Could it be that the Crystal under Silver Tear Lake is actually Zodiark, That the Lake Seal is His Binding, and Midgardsormr arrived on Hydaelyn DURING the sealing of Zodiark and said Sealing is what made the Lake out of the Aetheric Well it supposedly poured out of, thus causing Hydaelyn to charge Midgardsormr with protecting the seal over the now bound God in exchange for allowing him and his Seven Eggs to dwell there?

Well, I guess we'll just have to wait for 3.xx to find out since the Devs said all would be revealed in the 3.xx story cycle.