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CONTAINS SPOILERS
Start at Act 1 or Act 2 after finishing the game
The game is broken up into two Acts. Act 1 begins in the Overgrown Ruins and Act 2 begins in the Echoing Ruins: Act 1 consists of Biomes 1 to 3. Act 2 consists of Biomes 4 to 6. When you finish the game, you can start a new cycle from either Act. A new door opens up in your ship (Helios) left of the computer terminal. Enter it to be transported to either Act depending on which one you start at.