Several different ideas have been tossed around regarding the plot, and I'm pretty sure different people have different concepts of what's going on. Here's what we know:
1. The flow of mana to Aer from the Gloaming (that's what I've taken to calling the land under the clouds in my head) has started to stop. It has been hinted that the residents of the Gloaming are cutting the Aerans off intentionally.
2. The Gloaming creatures are upset with the Aerans for draining their mana for centuries, and, though they don't all get along with each other, want to take out the Aerans.

Here are some things we have yet to decide or are contested on:
1. Are the Aerans aware of the presence of the Gloaming before Aer begins to fall?
2. How do the Aerans view the Gloamlings? Are they afraid of them? Do they look down on them, like gods? Or is it some mix of the two?
3. What role does the planeswalker fill in this set? Is it Gideon? Is there a planeswalker native to Aer?

I have a new proposition for the first set that lets us pave the way better for a second set. I believe that in the first set, the combat should have yet to begin. The first set should involve the Aerans disovering, for the first time, the land below the clouds. In this scenario, it's not truly Aer vs. the Gloaming, but the different facets of the Gloaming fighting each other and Aer observing. There could be hits of the Aerans discovering that this land below is where all of their mana comes from, and some foreshadowing that things are about to go poorly for them.

My only issue with this is that it seems sets always start at the beginning of conflict.

How's this for a radical idea - we start the first set in the middle of the conflict, then the second set is a flashback to the start :)

Have all official Magic sets had linear stories? I'm not familiar with many of the older sets.
Having a "prequel" set naturally creates issues with the design of the second set. Usually, the small set develops the themes presented in the first set, adding new twists on the mechanics and developing new mechanics. Having a prequel set would mean we'd have to make the first set feel like a development of the second somehow, and if we added a new mechanic, people would wonder where it "went" in the first set.

Could be done, I guess - aftermath, prequel, fall.

Early magic sets didn't really bother with having a story; there were novels of extremely dubious provenance - and it took them a while before settling down to having triple sets anyway.

@cmeister: I really like that idea, but it seems like something to build an entire block around. Kind of like how one of the major themes of Pulp Fiction is a sense of being lost in the movie's timelines. It's a big part of what's going on, and was probably scripted that way from the start to make the most sense after being chopped up.

@Vitenka: Early magic definately did have compelling stories. The authors for the books, however, were abysmal, and the connection between them and Design (which did flavor back in the early days) was non-existant. Still, Antiquities, Homelands and Fallen Empires have very strong stories for small sets. They just never got good books.

In fact, if you want a non-linear story to base anything off of, you'd go to Urza's Saga. After having followed the Weatherlight through 4 expansions, heading all the way back to the tail end of Antiquities was an interesting leap. By the time the Urza Block was done, Magic was set up so that Both Urza's and the Weatherlight Crew's timelines were going off simultaneously in Masques block.

Yep, I agree that you probably want to base a block around it. I was just throwing some ideas around. :)