Necron, and the death of the Iifa Tree weren't necessarily unexplained. Necron, from what the game did tell us about him, (or at least hinted at), is the true form of the Iifa Tree, created by Garland to disrupt the flow of souls on Gaia, eventually leading to it's assimilation by Terra. As he did with Zidane and Kuja, Garland gave Necron a soul (why...?), it was because of this that he was able to observe the actions of Kuja, and it was because of Kuja's thirst for power and the devastation it left behind, that led Necron to theorise that life existed for one purpose only...to perish and return to the Zero World, a place that would be created by the destruction of the Great Crystal. Kuja's attempt to destroy the Crystal in Memoria after being told by Garland that he was not immortal as he had believed, only made Necron even more convinced that this theory was correct, thus he allowed the souls of Zidane & Co to enter the Hill of Despair so he could explain his theory and prove it right by destroying them and the Crystal. Defeating Necron put an end to the Iifa Tree.Originally Posted by Karellen
Necron, the inexplicable death of the Iifa Tree and Zidane's miraculous (and unexplained) escape from being turned into Genome pulp are the biggest ones. There are also a whole load of smaller issues like the details of Garland's plan, Kuja's sudden change of heart at the very end and most of the things that revolved around the Great Crystal that I felt were pretty poorly explained or poorly integrated with the rest of the game.
Garland's plans were merely to oversee the assimilation of Gaia by Terra, and create Gnomes that would be vessels for the souls of the Terrans once the assimilation was complete. Although why he tried to take Gaia by force, and why it put him back 5000 years is a mystery that they don't seem to touch on at any point in the game from what I remember.
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