Four thousand years prior to the main events of the Sonic series, the Knuckles Clanechidnas ruled a city on the site of what would become Mystic Ruins. The Clan chieftain, Pachacamac, attempted to remove the Chaos Emeralds from the ancient Chao shrine on the outskirts of the city. This angered their guardian, Chaos, who destroyed almost the entire Knuckles Clan civilization in vengeance.
Some remnants of the echidna city remained on the surface, where they were gradually overrun by the encroaching jungle flora. It is this swampy, ruin-studded rainforest which forms the modern-day Mystic Ruins.
The Mystic Ruins first appeared in Sonic Adventure. In this game, a group of archaeologists have gone to the Mystic Ruins to explore those ruins of the Knuckles Clan's city which remained on the planet's surface. Unfortunately, they were not prepared for the crash landing of Angel Island. Some of the archaeologists have gotten themselves lost in the maze of the thick jungle that surrounds the Shrine of Knuckles's race, while the others who had stayed behind, near the Mystic Ruins Train Station, built a log cabin to make camp. The archaeologists who built camp are constantly worried about their friends but are to afraid to go in the jungle to find them. If Sonic and his friends find any of the archaeologists that are lost in the forest they will state that they cannot find the ancient shrine or their way out, they however kindly refuse the help of the heroes saying it would not be very adventurous.
During the events of Sonic Adventure, Angel Island crashed back to the surface of the planet, on the shoreline next to Mystic Ruins; but it floated away again after the Master Emerald was restored.
In Sonic Forces, after getting the Phantom Ruby, Dr. Eggman tested its power on Angel Island, seemingly restoring Pachacamac's village to what it looked like thousands of years ago. When Knuckles and Silver noticed the village, Silver saw something rise from the Master Emerald. Knuckles told him that it was just Chaos, and that it was harmless. Much to the contrary though, Chaos proceeded to punch Knuckles, prompting the echidna and Silver to battle Chaos. When Silver caught Chaos in his telekinesis while Knuckles delivered the final blow however, Chaos suddenly disappeared, along with Pachacamac's village, leaving Knuckles bewildered.
Knowing of the transportation of Angel Island to Earth, the President's advisors planned to turn Mystic Ruins into a tourist attraction in order to boost the economy. Knuckles and Sonic were later shown the past of the Mystic Ruins by Tikal.
↑Stratton, Bryan (17 June 2003). "Knuckles The Echidna's Adventure Fields and Action Stages". Sonic Adventure DX: Director's Cut: Prima's Official Strategy Guide. Prima Games. p. 76. ISBN 978-0761542865.