A secret door is a special portal leading to a hidden area on a planet in Spectrobes: Beyond the Portals. Secret doors appear in place of normal excavation symbols on the map. They have a large hexagon shape and feature one of the three Property colors. A secret door can only be entered if Rallen is currently using a Child Spectrobe of the Property strong against the one reflected by the door's color.

The room within a secret door is a small cavern area, with the ground reflecting the features of the planet. Within the room the player can generally find rare minerals (such as Chroma and S Property minerals) and Mystery Stones. A text message appears on-screen when all the excavatable items have been found.

Opening the mystery door in a location can only be done once, but it appears to make the rarer minerals more common and increase the average rank of the common minerals.

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