ADAM, Megazone 23 and the other Megazones
Megazone 23 and the one called by the former "Dezalg" weren't the only Megazones out there and not the only ones trying to return to Earth after the five centuries in space, but after seeing what ADAM did to the aforementioned Megazones ("Dezalg" was annihilated and since ADAM was occupied with "Dezalg" at the moment, it sent Megazone 23 the self-destruct signal, which the humanity on it survived only by the skin of their teeth), they knew that trying to get past an ADAM that is still alive and kicking is complete and utter suicide, so they waited, trying to get by with the resources of the outer planets and the asteroid belt ("Oi, beltalowda!!") and working on the development of a weapon that one day could take out ADAM and open the door to Earth for them. But the centuries came and go and there still was no way to get past ADAM... Then EVE happened, she went up to the Moon and did the impossible: She reprogrammed ADAM with her, Eji's and Shougo's life data, who then deemed not only humanity worthy of leaving Eden, but also the rest of humanity to join in on the action of restoring Earth to its former glory the environment-friendly way (Eve was ready to lay down her life to get it done, but ADAM judged her worthy, as well, and tasked her with coordinating with the EVEs of the other Megazones, so all Megazones would pull together and wouldn't try to go at each other's throats, which caused all that mess in the first place). The fake Tokyos beneath Shogo's were once real ones unto themselves until the Dezalg attacked.
Those living in these replicas were conditioned to believe in what Shogo believed, unaware of another Tokyo right above (or below) them. However, the enemy attack would cause a breach out into space and render the area inhabitable. They were either evacuated to Shogo's Tokyo or...