I know this one isn't exactly an original theory – since House of Wolves dropped, we've come round to the idea that we can work alongside the Fallen in some capacity (hello Variks). However there's a couple of points that lead me to believe we'll fight alongside, rather than against, the Fallen in Destiny 2. Perhaps we'll even fight as the Fallen?
So, by now everyone will have hopefully read Ghost Fragment: Fallen 6. http://www.ishtar-collective.net/cards/ghost-fragment-fallen-6 The field report discussing how the Fallen have abandoned the Cosmodrome, Moon and Venus, discarded their weapons and banners and disappeared. Quite a big development for a enemy we've been fighting against for centuries! Have we finally hit them hard enough that they've retreated?
Perhaps. We'll see them again, no doubt about that. With no House allegiance, will they work alongside us under Variks?
If they do, I think there will be more to it than that. Here's why.
Let's remind ourselves why the Fallen are fighting us in the first place. The Traveller. The Great Machine, as they call it. It came to them first, and brought about their own Golden Age. Then it abandoned them, their society collapsed. They became thieves and scavengers. They followed the Traveller, looking to reclaim it. Followed it all the way to Earth.
They've been fighting us to reclaim the Traveller for their own. They're not agents of the darkness, like the Hive. They don't attack the Traveller directly. They just want some of that sweet sweet Light again. They want us gone, and want the Traveller to themselves.
So why have they stopped fighting us? Why the change of mind?
The Cabal are attacking the Traveller. Hard. Look at that damage!
And why? Because the Cabal are sick of us resurrecting. They've been investigating the Light, our abilities, and how to stop them. They attacked the Dreadnaught with the sole purpose of capturing high ranking Hive, so that they could find out how the Hive put us down for good. http://www.ishtar-collective.net/cards/ghost-fragment-cabal-4?highlight=cabal
So the Fallen see the Cabal attack the Traveller. They see us attacking the Cabal in defence.
Which side do they pick?
TL;DR – The Cabal are getting all up in the Traveller's face and the Fallen be like hell naw