Crono and his friends awaken to find themselves in Ioka Village in 65,000,000 B.C. Ayla explains that she found them laying in the Mystic Mountains hurt. So the Time Gate in Magus' Lair ended up transporting them back to the Prehistoric era. But Magus was nowhere to be found.
After resting and regaining their strength, they find that Laruba Village to the north was in ruin, due to an attack by the Reptites. So Ayla decides to travel to the Tyrano Lair to defeat the monsters once and for all. Crono's party follows her to the Dactyl Nest where they ride the Dactyls across the map to the Tyrano Lair.