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.
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Tails's workshop/house can also be found in Mystic Ruins. A train station has also been built, to serve the archaeological sites. 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.
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Tails's workshop/house can also be found in Mystic Ruins. A train station has also been built, to serve the archaeological sites. 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.
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Train station: A tall wooden building with stairs that leads to a stone bridge where the train waits for passengers to take to Station Square. Inside the building is a ladder that leads to a raft that takes people to the Egg Carrier.
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Tails' Workshop: A small two-story house located on a hill. It has with a long biplane runway with two rows of palm trees leading out into the ocean. The workshop is apparently connected to a cave beneath the house, where Tails works on his Tornado 2.
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Lake: A small lake with a waterfall leading to it and a river leading into the ocean. A Silver Chao Egg can be discovered by pushing against a panel.
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Caves: The west caves lead to Angel Island. The east caves lead to an Level Up Item for Knuckles and the Mystic Ruins Chao Garden.
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Chao Garden: A large grassy area on the side of a mountain. There is a lake and several large rocks lying about. The lake is connected to a larger one which is above the waterfall, it is there where Chaos 4 was fought.
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Windy Valley: A windy Action Stage where tornadoes easily form. The second part of the stage consists of floating paths high above the clouds.
Jungle areas

The jungle area is a maze-like area with many paths through a large jungle. Several archaeologists are lost there.
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Big's House: A small wooden structure where Big the Cat lives.
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Shrine of Knuckles's race: A large mayan-like temple that used to be the holy site of the Echidnas. It is the portal to Lost World.
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Lost World - An action stage set inside the temple. It is extremely large, and one part somehow features an outside section that looks nothing like the jungle. The temple also contains various booby traps such as a giant rolling stone ball and gravity panels that move on the wall. The center of the temple contains a mural of Perfect Chaos.
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Sand Hill: A long desert slope with various ruins which burst from the ground. (Could be Sandopolis as it's in the direction of Angel Island.)
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Final Egg: Eggman's large tower base, where he keeps his Egg Carrier and Egg Viper. It is entered via a long tube in the jungle, this is the base that the first of the E-100 series was created. The base is heavily defended and has three sectors, the first is simple pathways with spinning iron, spike balls and grinding mechanisms. The second drastically changes from the first, it is basically a large shaft that leads downwards, three tunnels lead to different levels and at the bottom there are more spinning masses. The last is similar to the first, except for three large rooms containing exploding crabs as well as pitfalls.
Angel Island areas
After Angel Island crashes in Mystic Ruins, most characters can access the island via a windy cave. The main area is a long corridor that leads to a large area where the Master Emerald can be found.
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Altar of the Emeralds: The ancient altar where the broken Master Emerald is, the altar is now broken and worn down due to extreme age. The Altar now stands on a small piece of ground which is separated from the rest of the island. Only by flying or using a wooden bridge, which was apparently built by Knuckles, can the altar be reached
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Ice Cave: A frozen cave with a lake that leads to Ice Cap.
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Ice Cap: A cold, snowy mountain with many caves which contains a frozen lake and a large number of satellites. The second part of the stage consists of a long hill for snowboarding. The slope is used for skiing.
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Red Mountain: Another mountain of Angel Island, except this one is volcanic. It is surrounded by smaller mountains–most of them are connected by metal bridges. There is also a large network of underground tunnels and caves which are flooded with lava.