What is Necron?
Garland explain to us, what he is. When Zidane is talking with him in Pandemonium, Garland said that the principal part of the Lifa Tree was not located in the physical world. That obviously mean, that the energy source of the tree was in the spiritual world.
When Kuja used his Ultima in the Crystal World, the heros died. Then, in the world of the deads(spiritual world) they fight the energy source of the Lifa Tree(Necron). This is why, when Necron is destroyed, the Lifa Tree die. And if you see Necron's face, you will see that he have the same face, that that faces in the wall of that temple that you fighted Ark(the faces talked with you). They were created by Terrans, exactly like Necron.