Quote Originally Posted by Jaywalker View Post
First, keep thinking back to The Twinning and how a variant of Alexander wound up being the boss. At the time just kind of went "oh that's odd" but looking back I think that's going to be really significant. Emet-Selch had a whole conversation with G'raha about how the Crystal Tower and Allagan technology by rights shouldn't be enabling time travel or interdimensional physical teleportation between shards as the WoL/D manages. And G'raha gives a weird non-answer when he asks.
If you read the text nodes scattered through the second leg of the Twinning, it discusses how the Ironworks was tackling the problem of how to travel through time (which would be necessary, to undo what had been done) - and that they found a potential solution based on a study of Primals. Retrospectively, I suspect that research mostly focused on one Primal in particular: Alexander, who became the template for the final boss. How they were able to study Alexander while he's sealed away is unclear, but it was definite foreshadowing for the final boss of the dungeon.