Planet (Geographical changes)
What are the geographical changes between the eras?
One supercontinent exists, akin to "Pangea" in our own history. Lava flow is still active, meaning more land could be made. However, the flows presumably stopped soon after this date.
The continents have broken up roughly to the formation seen in the modern era, though the Choras continent is actually connected to southern Zenan, and Medina is a little more right than its future position. After Zeal fell, everything but the future Medina continent; eventually, the water levels returned to normal.
The contents have aligned in four areas: northern Zenan, southern Zenan, Medina, and Choras.
The land Magus's Lair was situated on sunk in the last four hundred years, while the Giant's Claw rose up from the ocean floor. Truce Canyon has disappeared (apparently eroded) and Leene Square sits in its place.
The incomplete 1999 A.D. map is not reliable, as it uses the 1000 A.D. design (yet future civilization as shown in 2300 A.D. has infrastructure that could not exist in that configuration).
Several changes have taken place by 2300 A.D. Medina has seemingly rotated to the upper left counterclockwise to link with northern Zenan, whose left shore has eroded. This rotation does not include the area where Melchior's Hut was situated, as it now contains the Keeper's Dome and Sewer Access. Southern Zenan is largely missing, though evidence suggests it still existed before the apocalypse (the presence of a ruined skyscraper at the Sun Palace, which rose from the ocean floor). Apparently, Lavos's eruption decimated southern Zenan. Lastly, the continent of Choras is almost completely wiped out, save for the Geno Dome, suggesting that it also underwent duress from Lavos's eruption.
Trigger / Cross Images
The endings of both games depict the planet. Trigger's image shows the 1000 A.D. overworld wrapped around a sphere, while Cross seems to show a blurry El Nido wrapped around a sphere as well. See the El Nido / Planet Comparison image below.
From: Common Questions