When the Earth was destroyed by polution, humans migrated to Planet Zi. However, their time there was temporary. It was discovered a year before the humans left Zi that the planet was going to be destroyed. Thus they set out, traveling back to Earth. Throughout most of this journey the inhabitants of the Immigration Ships entered a cold sleep. The intention was for the ships to enter Earth's solar system and activate the Zi Forming Device, awakening the humans only after the Earth was inhabitable again. Zoids were imported to Earth and included in the Zi Forming device's blueprints, resulting in Zoids forming naturally in the ground. Bowman asserted that their strength would be essential for redeveloping the planet.
Before the ships could reach Earth, rebels rose up on the immigration ships. These rebels, coming from the Empire, insisted that they didn't want the Republic to reform once they reached Earth. They instead sought to claim the Earth for themselves. When Bowman realized that they intended to destroy the other ships, he changed the course of the Science Ship to veer towards a wormhole. The rebels scrambled to regain control, and Bowman and Sally both escaped in an escape vehicle. The Science Ship was pulled through the wormhole and arrived at Earth far earlier than intended.
When the Science Ship arrived at an Earth no longer in need of help, over 100 years in the past, the Zi Forming device activated. Rather than bring renewal to the planet, it brought widespread destruction, resulting in violent tectonic shifts and storm activity. This falty activation also brought about the existence of Jaminga and a sudden rise in Zoids that Earth had never had to contend with. The Zoids wreaked havoc in modern cities, with the Genospino being responsible for destroying a third of the planet in a single night. Some tapes of this destruction still exist today, restored by dedicated individuals such as Leo. It's the footage seen at the beginning of each episode.
The first of the immigration ships landed on Earth 30 years before the story begins. The first was the Republic ship, which landed a year earlier than the Empire's ship, giving them a head start in development. Discovering that the Zi Forming device hadn't properly activated, the immigrants needed to wear specialized masks to breath in the Earth's atmosphere. The second generation no longer required this technology.