why are monsters invading the cities?

[Punainen]

It's all still Canon, Atomos is summoning all these creatures through time/space.

Just because he is dead in our world, doesn't mean he is dead in others. Atomos simply goes to a time he was still alive and copy and pastes him back to life. It explains all the monsters and Naels that attack the city.

THIS. Final save doesn't necessarily mean the end of the storyline. They wouldn't bother changing the weather and stuff if the storyline was over.

[Majidah]

THIS. Final save doesn't necessarily mean the end of the storyline. They wouldn't bother changing the weather and stuff if the storyline was over.

this sounds more accurate if you ask me

Naels Aether appeared to be absorbed by Dalamud (you know, when he falls backwards after you defeat him and explodes into all that stuff that you watch float into Dalamud) - it merely appears to be a copy of him, rather than the original.

Whatever it is that is coming down with the moon, it is bringing forth all kinds of evil, and it is probably going to kill us all - notice that where ever Garleans have tread before since Dzemael Darkhold, everything they do seems to bring a trail of voidsent with them.

Whatever happened the last time they tried to pull Dalamud down destroyed an entire city in the Garlean Empire, around ten years back or so - who isn't to say that whatever powers causing it don't rip voidsent through into the world, clearly Dalamud didn't hit them last time round.

As to why they are attacking the cities, well if you haven't noticed they have been getting closer and closer patch after patch - and we still have an aetheryte crystal in each of our cities.

Also, this is 'canon', this is the reason that we are going to be sent to the future of "A Realm Reborn".