As others stated, Gaius and Estinien had been destroying facilities creating the Black Rose weapon and only stopped due to events occurring in the Capital. Zenos on the other hand killed his father to prevent the order for its use to go out. I am forced to wonder if the use of the weapon will be used as a tool for good in stopping some threat somehow later down the line though.
Here's my question though, are Emet Selch and Elidibus still alive in the original timeline? Is Minfilia? Hydaelyn? The Devs said that to understand where we are going we would need to look at Heavensward. They also said some things about making sure to do the Omega raid as well as Alexander. The Twinning is very much a amalgamation of both and the ramifications of the dungeon are immense considering it was what allowed the plan to become reality. In the dungeon we get both eScape as the dungeon music and Locus as the boss theme. This is important to note because eScape is about changing realities (going to the first) and Locus is about the dangers of time travel.
I once replied to a 5.3 prediction thread as follows.
I left it at that for awhile. But this latest tale made me stop and think about it some more. See, if we add Locus to the mix (again Alexander was recommended for higher understanding) we also get this bit.
Falling back right into the system of
Falling back on all that's erased
When fighting back right out of this system
Means falling back right into this space
Yes, falling back right in with the system
Who'll see you falling back to the end
When falling back is better than simply
Falling back into pieces again.
This makes me question if we aren't done with the original timeline. We currently have both Cid and Graha alive and well with all his memories on how to actually achieve time and space travel. I understand there is a few people who would absolutely hate that thought as it seems as though it's a bittersweet farewell to those left behind. I don't know, my theories are generally not well liked by a fair amount of people, but I am happy to find out either way.