Necron is some sort of flying demon (the Eternal Darkness) & it's one goal is to destroy life. You get Trance Kuja before him though.
It's alright, Andy! It's just bolognaise!
Necron, though he appears to come out of no where is in fact present through the entire game. Several of the characters are afraid of death, most notable Vivi, Zidane, and Kuja. Freya's little line in the prelude is even "To be forgotten is worse than death"
When Necron shows up at the end, he is basically the character a personification of death and the majority of the character's worst fear. You'll notice that you do not technically defeat Necron. The message is is that no matter how hard you try to fight death, it will come eventually.
The ending gives the characters hope and Vivi's final letter basically says to cherish the time they all have left.
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