Death and coping with one's own mortality are the main themes of FFIX, so a lot of one's enjoyment of the second half of the game hinges on whether this theme resonates with them or not. Vivi and Kuja display the two sides of the coin: both learn of their impending death, and become agitated. Whereas Vivi decides that the point of life is just to live it to the fullest, Kuja comes to view that life is pointless if you are just going to die. However in his final scenes it is implied Kuja has come round to the player party's way of thinking.

Necron is a surprise final boss, and is introduced as the culmination of the game's death theme rather than as a culmination of the different storylines coming together in the end, as one would normally expect. "Necron" means death and his Japanese name is "Eternal Darkness" and he wants to revert the world to a zero world with no life, not because he as the embodiment of death is evil, but because he sees the mortals' suffering because of their fear of death. If all life fears death yet all life will always eventually die, then life must be suffering. Zidane argues otherwise in his speech before the final battle, and seeing the party's will to live Necron dissipates. Necron being encountered on the "Hill of Despair" implies that the party was sent to the "death's door" by Kuja's Ultima spell, so perhaps the whole experience was more akin to a near death experience than anything else.

The whole Terra thing is part of the game-wide theme, in that Terrans sought eternal life, both for themselves and for the planet. Yet if you never die your memories never return to the crystal and your world will stagnate. Death is inevitable because only that way can new things be born. Terrans looking to live forever is what Kuja wanted and what I guess many people who fear death would want, but it would be against the natural order of things.

Death in FFIX is shown in somewhat comforting light with one's legacy living on despite you no longer being here. In the final scenes Vivi has died but leaves a heartfelt message behind that speaks of the meaning of being alive. Vivi's final words are "farewell, my memories will be part oft he sky" and in the ending you see "his sons". Mikoto thanks Kuja for showing Genomes can be more than just empty vessels, and thus Kuja's legacy lives on with the Genomes who were left behind.

The world is for the living of course, and thus the final moments show Zidane, who was thought perished, "returning from the dead", and everyone enjoying their new lives.