The implication behind what Varis intends to do is that, after all the Shards have been Rejoined, the people left will be of his "perfect master race," capable of taking on the Ascians and "freeing the reins of history from their grip." I... don't know what he intends to do about Zodiark, assuming he believes Zodiark exists at all - don't forget the Garleans are known atheists, so Zodiark may not be something he's taking into account.

Step 1: Cause all the Rejoinings to recreate the "perfect master race."
Step 2: Kill the Ascians.
Step 3: Profit!