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Robotnik claimed to have been looking for the zone for years, even before his conquest of planet Mobius. In this zone, Steve Owl led a small group of animals (including Benny the rabbit, Sammy the panda, and Sammy the hippo, among others) who wanted to remain safe from Robotnik.
Sonic the Hedgehog happened to land in the Hidden Zone after a battle on Robotnik's Sky Fortress. Robotnik followed Sonic's trajectory and was able to find the zone, to which he dispatched his Badnik army. Sonic was able to defeat the Badniks, but the Hidden Zone was no longer safe. Therefore Sonic led the residents of the Hidden Zone to the Emerald Hill Zone, where he promised they would find friends and be able to actively oppose Robotnik's rule.