Last warning, there're big spoilers.
When I first beat FFIX I was under the impression that Terra actually assimilated Gaia. But looking around I find that others don't seem to come to that conclusion, but infact believe Kuja destroyed all of Terra when he went into Trance.
Anyway, my evidence -
- How could Kuja destroy a planet? From what I saw all he destroyed was Bran Bal and some of the mushroom shaped structures.
- Before the battle with him in Trance inside the Crystal world he says: "Gaia's already doomed. Its assimilation by Terra has begun, and the Iifa Tree will incite a cataclysmic destruction of Gaia." Note that he says this after the so called destruction of Terra.
- After the battle with Necron Zidane goes to save Kuja from the Iifa Tree after it goes crazy. Why would the Iifa Tree do that? Seems it's still aiding the assimilation, to me.
- At the very end, before the words "The End" appear, we see a red sphere and a blue sphere (obviously Terra and Gaia) colliding into each other to form the crystal and the words "Final Fantasy IX".
So, what do others think?