After Crono slain Lavos, the Frozen Flame was found in the new timeline and Chronopolis was built.
In 2300AD, studying the Frozen Flame, Chronopolis' scientists wanted to use it to gain control over the whole time-space continuum. Belthasar helped in the process but planned everything so that someone could blabla etc. save Schala and all. He 'disappeared' some time after (in fact he went to the post-Time Crash's 1000AD~1010AD).
In 2400AD, when Chronopolis finally managed to trigger their 'counter-time experience', the Frozen Flame sent back Chronopolis some thousands years into the past, so that it would change History and give Lavos another chance of destroying the Planet!
But the Planet tried to counter this by bringing from a different dimension what was meant to be its masterpiece, Dinopolis, the futuristic capital of the Dragonians, descendants of Azala. Then the Polis War began, opposing Chronopolis & FATE vs. Dinopolis and Dragon God.
Dinopolis lost. FATE built El Nido etc. The Humans and the surviving Dragonians lived together *quite* peacefully (until Porre arrived in 900AD). The weakened Dragon God was divided in 6 by FATE using the Frozen Flame, and thus the real 'soul' of the DG was consumed by Lavos the Devourer of Time.
So, basically, the Time Crash sent Chronopolis into the past, and also brought Dinopolis from another dimension. And it then affected and changed the CT timeline.