This is a pretty interesting topic! =) Here is my opinion on how the original timeline went, just for funsies:
1. The Mystics destroy Zenan Bridge (as is mentioned in the game.)
2. Frog (alone or with Guardia soldiers) saves Queen Leene.
3. The Mystics ravage the southern continent, creating a desert.
4. Guardia repairs the bridge.
5. Ozzie attacks the bridge with soldiers created through necromancy, humans barely hold off/ Ozzie retreats after he deals significant damage.
6. Magus attempts to summon Lavos through a ritual. He is successful but creates a giant gate that engulfs his castle
7. Magus, Ozzie, Flea, Slash, the castle and the army inside are scattered throughout time or doomed to face Lavos. ***
8. With all command and control gone, the remaining Mystic army collapses.
9. Those that remain form Medina.
10. Tensions/grudges remain - some Mystics get over it.
*** If Ozzie was killed he must have had offspring beforehand (same for Yakra, as we see). If he was sent through time he was probably sent 100-200 years in the future and perhaps founded Medina as a collective. (His offspring is the leader of the Mystics in 1000AD - but that is only Ozzie the VIII and we see that Yakra's offspring is Yakra XIII. Different lifespan or time travel? who knows.)
If Magus was sent back to 12000BC as we see in the new timeline - the events of the Ocean Palace would have been different. Melchior would have been imprisoned on Mt. Woe and probably never freed. The Mammon Machine would never have been overloaded by the Ruby Knife, so Lavos probably awoke sometime later, when much more of its energy had been sapped. Since the Ocean Palace did not rise to become the Black Omen, the Queen would not have been in the Ocean Palace at the time of Lavos's awakening in this timeline - she would have died in the attack/survived and integrated with the Earthbound Ones eventually.
That's my take on it.
