Story Question (Small Spoilers)

[Tigmafuzz]

I always thought Necron was the spirit of the Iifa Tree or something. I never thought about how he might be connected to the Crystal itself. But either way,

Crystal = The entirety of existence.

No Crystal = no existence.

Therefore, Crystal.

This, basically. Also, since Necron's goal is to destroy the Crystal itself, logic dictates that Kuja failed.

EDIT:

When Zidane awakens on the Hill of Despair, he is greeted by Necron's voice emanating from rays of light above the hill. The entity announces that by observing Kuja's murderous actions it has come to the conclusion that all life exists merely to seek death. Necron resolves to destroy the Crystal, the origin of life, and thus revert everything to a "Zero World" of perpetual nothingness. It teleports the heroes to a coliseum-like structure and engages them in battle.
Though Necron utilizes a plethora of destructive magic, it is ultimately defeated. Kuja uses the last of his powers to teleport Zidane and his friends back to the Iifa Tree, and as Necron dissipates, it is shocked to find the power of the will to live is so strong. Nevertheless, the being pledges that it will always exist, as long as there is life and death.
In "Final Fantasy 20th Anniversary Ultimania - File 1: Character Book", Necron is described as, "a being awakened by Kuja's fear, despair, and hatred, which called out to it as he learned of his mortality, just as his ambitions were within reach".

So it could have absolutely nothing to do with the Crystal or the Iifa Tree at all, and just be a random entity that already existed in the universe lying dormant.

Although, since the game itself is all references to previous games, and Necron bears many similarities to Cloud of Darkness, it could be the physical manifestation or an emissary of the Void itself (or whatever the equivalent of the Void is in the FFIX universe.)