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(Sorry, I've been away for a bit. My thesis proposal, and then Thanksgiving chaos + some insane desire to marathon the entire Marvel Cinematic Universe = me being a bit out of it).

If this is the current idea of the threat:

Here's where the timeline could diverge, and it could be just that simple:
Discord plants the seeds. Celestia and Luna defeat him and seal him in stone. Luna never turns into Nightmare moon, and everything is hunky dory for a thousand years. No new Elements of Harmony are needed, Discord remains stoned. Then the seeds sprout, and what's the first thing they do? Capture Celestia and Luna, who are the only ponies who know about the Elements of Harmony in the first place.
None of the universes are anywhere near Season Four, so there's no reason for them to know what the heck is going on. It could be brilliant.

Then I approve as well. Love the concept.

That said, I think we should next determine what effect the seeds will have. Will it be just like the show -- spiky roots, spiky clouds, and misfiring magic, but otherwise everything's still okay, or some kind of more fundamental alteration?

LJP posted something awhile ago I really liked:

Actually... maybe it's... kinda like a glitched-out program. Maybe it looks like a normal universe, but there're things missin'.
Without an Element a' Laughter, the things that make folks happiest break down or disappear. Without Loyalty, promises get broken - not abandoned, but the universe itself jus' undoes it. An' without Magic, there are no heroes. Ponies who stand by their friends are forgotten, an' ponies who fight monsters only become monsters. That kinda thing.

And I think that could be a cool effect of the seeds. The seeds attacking the tree of harmony not just overrunning Equestria with wacky plants and clouds, but also fundamentally removing the harmonious qualities from the world, so laughter stops happening, promises being undone, etc.

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In other words, a bleak, hopeless land where the Cynical, weary natives fight a hopeless battle against giant plant tentacles.

2294439 Winner!

I'm liking this plan!

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ONOREEEE DICKEIDO!!!!!

EDIT: I suppose I should actually say something of relevance, hmm.....
Maybe they come together from something fairly unrelated to whatever's plaguing the world they end up in, but decide to help anyway?
I can't think of any concepts for the villain itself, but it's better than a generic "Discord did it" plot. Or, maybe the villain did cause it, but not directly. It's hard to take seriously a villain so stupid as to purposely bring to them a large group of heroes with great moral code.
Also, I'm in favor of having multiple groups, and by the end of the story (Not too early, but not too late, similar to Crisis on Two Equestrias), we have every Element Bearer from the nine- er, six worlds working together to defeat the villain.