The Kingdom of Zeal, let's start there. Queen Zeal is obviously getting her ass booted out of that position, and Schala would take over. Racism fades, and the Earth Dwellers get to chill out in Zeal ^_^ Zeal falls back on the Sunstone cause it's cool like that, Melchior and Janus get to chill out in 12,000 BC, and history would be changed.
600 AD. No Janus, no Magus, no war between Humans and Mystics. Thusly the two races can live in peace. Hopefully Zeal can chill out too. Masamune thusly never breaks and the sword can chill out on it's mountain bachelor pad. Glenn never becomes a Frog and Cyrus never dies.
1000 AD. Not much changes. Um...I guess Zeal can back up Guardia in that Porre invasion stig. Thusly, Masamune remains uncorrupted(?). The Time Crash doesn't occur, and FATE isn't corrupted. Thusly, none of the events of CC happen. Especially since there's no Time Devourer. Thusly Lucca, Serge, and everyone else can live peacefully.
2300: See CT's ending.
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Damn, I wish they DID defeat Lavos at the Ocean Palace now.