The Guardians of Destiny are examples of further clarification and exposition on the fantasy Gaia Theory which serves as the base of the world building of FFVII, and by proxy, FFIX and FFX. Because all three games by their nature share similar concepts which each other. These "whispers" are the spiritual embodiment of a deterministic will that shapes the future of a planet and it's life.
Spirit Energy is the flow of life that connects all living entities that exist on a planet. Composed of souls that have died and are yet to be born, it continuously cycles back and forth at the margin of life and death. This flow in FFVII is called the Lifestream, and while it can be harnessed as energy called Mako, that's only it's physical form. The true nature of the Lifestream, is the planet's collective life force.
A planet is defined by its Lifestream. It's spirit energy. And by that logic, planets are alive and carry within them a will and consciousness. This is shown by the Cetra who speak to the planet and in turn listen to it. Its this very will that dispatches Weapons to protect itself from threats to its existence, and even casts judgment on humanity via Holy.
In CC we see that the Planet's will, the will of the Lifestream, can be embodied in a singular divine entity, aptly named "The Goddess." The Goddess Minerva is in essence the strongest, most powerful summon that is invoked by the Lifestream itself. She is a spiritual manifestation of the collective will of the Planet.
In essence, the collective consciousness of all people created their goddess, and in turn the goddess functions as their embodiment and will. An on the nose statement regarding history and mythology.
And in DC, we see Omega. The ultimate ark of planetary self preservation that is meant to ferry a planet's life force so it can be reborn anew in the cosmos. This reveals that the spirit energy cycle plays out not just on a planetary level, but a cosmic one. Planets cycling back and forth between life and death so they are reborn anew elsewhere in the stars.
Suffice to say that a planet's own existence plays out much the same way as a human's. Albeit on a macro scale. It lives, struggles to survive, and then when it nears its end, it's life joins the cosmos and seeks to be reborn elsewhere to start the cycle again.
However, the one thing that stands out against this entire cycle is Sephiroth. His mind and spirit subvert the natural flow of life by not only maintaining it's ego within the collective consciousness of spirit energy, but by acting from behind the veil. The entire cycle of life is premised on the living making the choices and experiences in life, and then rejoining the Lifestream.
But what if a force within the Lifestream could work the process in reverse?
Sephiroth corrupts the Lifestream, and by extension, the very will of the planet. If Sephiroth were able to fully subvert the entire planet's natural order and determined path of life and death, his will would become the Planet's will. Which in turn would forge the fate of the Planet's spirit energy. A new destiny with potential to create hitherto unrealized life. Thereby, he creates the mechanisms of the planet that in turn work for him for their own benefit.
As seen OTWTAS Lifestream Black, Sephiroth's hatred for the planet and it's order, draws out spirits steeped in hatred. These spirits fuel him and become his "Negative Lifestream" seen in Advent Children.
So what if this new potential future for the planet and it's life, becomes the Planet's assumed Destiny to pursue? And this newly corrupted spirit energy now wishes for Sephiroth to be their makeshift god and grant them a new and until now, unforeseen potential future? A newly established impulse and desire to self destruct all to be reborn and ushered into a new life with Sephiroth as their god. A whisper towards destruction and damnation.
The Guardians of Destiny serve as embodiments that pursue the determination of a planet's fate. They appear as unborn corrupted spirits that wish to protect the course of Fate that presents to them the chance to see their future made real. A sort of thematic inverse of an unsent/remnant. Instead of a being resisting death to stay alive, they're as of yet unrealized future spirits resisting death in hopes of being born.
Destiny doesn't have to necessarily imply literal time travel, only the perceived and inevitable fate that the choices through time thus far have laid out that must be adhered to. Sephiroth giving the weakened, dying planet and it's potential spirit energies a new destiny, would be horrifying yet fitting given the nature of his powers. And in turn, the planet and the potential spirits clinging to Spehiroth, now wish to protect that Destiny. Because he's on his way to becoming a god.
And if anything, this new plot thread concisely connects to Sephiroth's original plan to ascend to godhood. It clearly establishes that Sephiroth is working on a level beyond the physical and beyond the motivations of just a malevolent alien invader. Jenova is now but one means for Sephiroth to reach his divinity. The other, is the very planet he wishes to kill and then remake in his image.
It certainly cements the "birth of a god" theme of his plan and leaves no question as to who is in control between him and his mother.