Because I don't want to imagine that the Whispers have been around forever, guiding every event since the planet's birth, I much prefer the notion that the inciting incident for all this timey wimey-ness was Sephiroth's defeat in Advent Children.
AC Sephiroth, in all his uniqueness and defiance towards becoming just a memory, achieved the impossible: He cut a hole through spacetime. AC Sephiroth travelled through this hole, bringing along his remnants Kadaj, Loz and Yazoo, and successfully stepped outside the boundaries of time. This effect rippled through past, present and future.
The planet's defenses against time-breakage were limited. The Time Guardian, familiar from the Temple of the Ancients, was one of few entities to observe this event. From being a singular-timeline planet, the Time Guardian observed how the planet's history shattered into millions of fragments. As a guardian, their role was to ensure the consistency of time: A singular timeline. That is their axiomatic purpose, whether a multi-timeline be catastrophical or not. So the Time Guardian created the Whispers: Entities that would travel across these millions of new timelines, correcting events and trying to weave everything back into a singular timeline, turning the shattered mirror into just the one mirror.
The process was not perfect and inconsistencies remained, like the design of Stamp the dog, due to the timelines still not coalescing into the one. The Whispers also attacked AC Sephiroth and his remnants. They were successful in taking control over the remnants, turning Kadaj into Whisper Rubrum, Loz into Whisper Viridi and Yazoo into Whisper Croceo. AC Sephiroth escaped, or was too powerful to be subdued, and his exact plans remain unclear. Having upgraded from a traveller of the lifestream to a traveller through time, AC Sephiroth now has more cosmic knowledge than ever before. Just as Sephiroth had used Cloud as a "core"
to remain alive in the lifestream after the events of OG, Sephiroth now re-employs Cloud as a
constant to give himself purpose in this cosmic, chaotic, multi-timeline mess.
With the Whispers defeated at the end of FFVIIR Part 1, and the ensuing explosion happening simultaneously throughout every timeline, the planet's multiverse status will worsen, until paradoxes occur, timelines/planet-verses dissolved and ultimately the planet is erased from history. Just like spirits dissolve in the lifestream, so too will time dissolve into the greater cosmos and nothing will be left of what was, is or would be.
Whether this could affect the entire universe or just the planet is unclear. Though IF the events of FFVIIR jeopardizes the existence of the entire universe, then the erroneous promotional tagline from the PAL box of the original FFVII will finally have become real.
"Cloud Strife a cold-hearted mercenary, accepts a mission from a group of eco-warriors, unaware that it will lead him on a journey that will change not just his life, but the lives of every soul in the universe...."
The only way to solve this time crisis is via the ultimate deus ex machina: Holy. The only magic that can erase Weapon, Meteor, humanity all in one fell swoop is also the only magic that can reunite all the planet's time shards into ONE. Aerith will be praying at the altar not just for the eventuality of Meteor being summoned, but for the historical existence of the planet itself.
Most everything will play out the same as the original game, only with all this needless fluff added. Though one crucial thing may end up different. Because AC Sephiroth (now fully merged with his non-time-travelling self/selves) will end up defeated outside the bounds of time, at the edge of creation, there won't even be any planet for Sephiroth's spirit to return to and defiantly carry his will. He will truly, and ultimately, be defeated just before Meteorfall, same as we originally thought that he was after the original game. Geostigma will not happen. Sephiroth will not return. This, in my opinion, is a way to make the ending feel satisfactory. When you know that people are going to fall down dead from Geostigma for a period of two years after the original game, your sense of victory is lessened. With the FFVIIR series, we might prevent Geostigma from ever even happening.
The final, coalesced timeline, with all its victories and tragedies that this entails, will mean the ultimate end of Sephiroth (and by all likelihood, Jenova).
