OK, having read through Mako's excellent post reflecting on the ending, here's what I think about the Whispers.
Presumably they're called Whispers because they represent faint voices of warning or guidance. They're manifestations of the planet's will - I'm imagining the planet/lifestream murmuring "yes", "no", "don't", "this way", "stop" etc.... I don't know if they are meant to represent the voices Aerith heard in the OG, or something different. The planet has a plan for its own future and wants all its lifeforms to conform. As long as their actions don't mess with the planet's plan, they are free to do as they like, but if they screw with the main program, the planet will nudge them back into line.
But this begs the question: unless the planet actively wanted to get cancer, why did it allow Shinra to rise to power, process mako, and create Sephiroth? Why didn't it get one of the Whispers to smother President Shinra when he was still a baby in his cradle?
Maybe because the Whispers weren't active then? Maybe they are like the Weapons, dormant 99% of the time, but activitating if a major threat presents itself. Maybe, like the Weapons, they were created by the planet specifically to tackle the mortal danger posed by Jenova - and so, when Sephiroth's will starts manifesting itself through the Jenova cells in the clones, the Whispers spring to life like so many white blood cells alerted to the presence of a pathogen.
Jenova and the planet are alike in that both are semi-sentient, multi-cellular organisms. For the planet, human beings and all other lifefoms are just like our hair, skin, eyes, and all out other different types of hair are to us: manifestations of its essence. Ultimately, all lifeforms are reunited with the planet in the lifestream. The difference between the planet and Jenova is that the planet is self-sustaining when it comes to life, whereas Jenova is a predator that needs to consume others to live.
Since Shinra is "not the real threat to the planet", that would explain why the Whispers didn't put an end to President Shinra before he could do any harm.
Here's the thing about fate, though. If it can be altered, it's not your fate. if your actions can't alter your fate, then you are not in control. It's a paradox. In Greek tragedy, knowing your fate is itself the curse, because everything you do to try to avoid it only brings it closer, and in the end, you by your freely chosen actions bring your own fate down on your head. I’d like to think that’s what is going to happen with this story. But I doubt it. The point is, knowing what your fate is doesn’t mean you’re in control of it.
Mako said that
I think it's clear from Aerith's own words and the groups agreement that they all went into the Singularity with the intention of defeating Sephiroth. That's what Aerith clearly states, however, they all unwittingly cross swords with the Whispers of the Planet. They intended to protect the planet and the Whispers but because of their opposition, they fought them seriously and defeated them. In doing so, the Planet became vulnerable. And Sephiroth literally absorbs the Whispers into him and creates the future. The new destiny for the planet. A giant meteor slamming into Midgar.
So maybe that was Sephiroth’s intention all along, since the Whispers were impeding his will. Get the good guys to eliminate them.
From the way the fight went, Whisper Harbinger holds the planet's "future/fate" (or glimpses thereof) within itself, but with it's defeat Sephiroth eats it and... We see Meteor and end of the world. From this point, Sephiroth controls fate, because he absorbed the entirety of the Whispers, just like at the end of OF FFVII when he absorbed the Lifestream.
So if Sephiroth controls fate, Cloud & Co need to wrest that control back from him.
Why, exactly, do we see Meteor? What mechanism is functioning here? Are we meant to suppose that the planet/whispers are privy to the hopes and dreams inside Sephiroth’s mind? Or does Sephiroth allow us to see it because he wants us to follow him and try to stop him? The Planet tried and failed to stop him; now it’s down to our plucky band of rag-tag misfits?
*I do also think that this ending has set SE up nicely for creating and selling an endless stream of DLC alternative timelines in infinite variations: Zack lives; Zack dies; Aerith lives; Aerith dies; Rufus lives; Rufus dies....
