During the Great War, the Kingdom of Acorn's chief magician Ixis Naugus decided to create a safe haven for himself in order to avoid the ensuing carnage from the war. He also desired a place where he could hone his skills of the elements. Thus, Naugus created the Zone of Silence. After successfully disposing of the Overlander Nate Morgan with his partner Kodos, Naugus withdrew to the Zone of Silence where he would wait until the Great War's end before re-emerging. However, Kodos had the portal locked so Naugus could not escape.
When Kodos attempted to take the Overlander Julian Kintobor under his wing as a future partner for his planned takeover, Julian betrayed Kodos and sent him into the Zone of Silence, as he already had plans to take over himself. Julian informed King Max that Kodos had died when he tried to use one of Naugus' devices which he didn't fully understand. Julian replaced Kodos as Warlord, and began planning his schemes.
After the Great War's end, Julian began his military coup to overthrow King Max. With the king captured by his SWATbots and the majority of Mobotropolis' citizens being rounded up for roboticization, Julian informed Max he changed his name to Dr. Ivo Robotnik, and banished Max to the Zone of Silence.
During his rule, Robotnik found himself at odds with the Original Freedom Fighters. However, after bribing one of its members, Private Trey Scales, Robotnik managed to lure the group into a trap. He roboticized the whole group, including Trey Scales, and banished them to the Zone of Silence.
Sonic the Hedgehog and Sally Acorn managed to enter the Zone of Silence and bring King Max back to Mobius Prime. The king however slowly began turning into crystal, a side-effect from his alliance with Ixis Naugus to survive in the Zone's harsh conditions. When Dr. Robotnik was killed, Naugus managed to escape from the Zone of Silence as well, due to the Ultimate Annihilator weakening the dimensional barriers. Naugus was accompanied by Kodos and Uma Arachnis. Naugus had hoped to establish himself as Mobius' new king, as he made a deal with King Max in the Zone that he would save his life in return for Max making Naugus king. However, Sonic and the others refused to accept this, and defeated Naugus.
When Sonic and Tails give chase to Naugus, the find themselves facing the wizard at the home of Nate Morgan in the Southern Tundra. Naugus attempted to merge Nate's home with the Zone of Silence so he could use his omnipotent powers to defeat Sonic and Tails. His efforts fail when a trove of Power Rings Nate Morgan had result in the two heroes transforming into Ultra Sonic and Hyper Tails, though Naugus also transformed into Ultra Naugus. With the help of Nate Morgan, Naugus was once again trapped in the Zone of Silence.
Roughly two years later, Naugus was freed from the Zone of Silence when the children of Uma Arachnis - the Arachne - used the Sword of Acorns to cause a dimensional rift in Dr. Eggman's Egg Vineyard and free him, while the victims of the Egg Grape Chambers were pulled into the Zone. The dimensional rift also resulted in the death of the Ancient Walkers.
When Eggman's computer-virus "son" A.D.A.M. used Shadow the Hedgehog and Tails to draw all of the Chaos Emeralds in the universe to Mobius in order to use their powers to finally defeat Eggman's enemies, Eggman freed the two while Sonic kept A.D.A.M. busy. With the energies of the Chaos Emeralds empowering them, Turbo Tails and Super Shadow worked together to send all of the Chaos Emeralds into the Zone of Silence, thus fulfilling the "Great Harmony" as prophesised by the Ancient Walkers.
With Feist as the only known being still in the Zone of Silence, he used the limitless powers of the Chaos Emeralds to warp it into the Special Zone and modify it to how he desired. Sonic and Tails entered the Special Zone to ask Feist for one of the seven Chaos Emeralds he formed to save the dying King Max. Feist granted them the grey emerald due to Sonic's efforts in defeating Feist's former master Ixis Naugus, but warned the two that if they returned, he would test them before giving them another Chaos Emerald.