In the Subspace Emissary
The most common doors are red in color with a pointy top, with blue light shining out from the edges. They transport the player to the next room and act as checkpoints if the player runs out of stocks and uses a Continue (the player will respawn next to the door they had last entered). Most doors lead to the next area and are one-way, but some lead to special rooms which often contain cubes.
Some stages feature doors with distinct visual designs, although they function identically. In all stages set aboard the Halberd, the doors are bronze in color, and slide open instead of opening from the middle. In the stages which feature the Research Facility and the Subspace Bomb Factory (i.e. the Isle of the Ancients), the doors are a metallic silver color with glowing lines. In the Subspace stages, the doors will open like the red ones but are purple and have what appear to be scales on it. Uniquely, two areas in the Subspace Emissary are entered without doors: in The Ruined Zoo the player enters a building through a hole in the wall, and in The Lake Shore they enter a cave through a large opening in the cliff face.
Doors increase the player's clear percentage: to reach 100%, all the doors in all the levels must be entered. Three red doors only appear after the Subspace Emissary has been completed; these lead to special battles the three challengers that have not appeared in the Story Mode: Toon Link, Wolf, and Jigglypuff,. Defeating these characters will make them join the party and the player will unlock them, if they're not unlocked already.
In The Great Maze, several special-looking doors can be found:
In some stages, the end of the level is illuminated by rays of light. Entering the light will make the screen brighten until it turns completely white, at which point the regular finish screen appears. If the stage is completed again, the light will be replaced by a golden door.
In The Lake and the part of the Great Maze based on The Forest there are day-changing doors that are yellow or sky blue with a triangle in the middle. Entering one of these doors lead the player to an area very similar to the one they just left, but with some key differences, like the overall color scheme, the enemies present and what blocks are breakable. The actions of the player in one version of the world also affect the other: for example, it is often necessary to destroy blocks in one version to make them disappear in the other.
Triple switch doors
In the Subspace Bomb Factory, there is a locked metal door with three lights on it. In the same area there are three lever-switches (blue, red, and green): hitting them sends a visible signal to the door and makes the corresponding light on it activate. Once all three switches have been activated, the three lights as well as the edge of the door will shine and the player will be able to pass.
There is also a triple switch door in The Great Maze, in an original area of The Research Facility. This door functions identically to the previous one, except that the door itself is shrouded in dark mist, indicating a Boss Battle. However, unlike the first case of such a door the three switches are located in three different rooms, instead of all being in different parts of one big room.
Hidden doors are doors that are not necessary to enter to clear a level. For example, a door might only appear right after it has been passed by, a switch must be pressed to make the door appear, or it is hidden in an unexpected place, such as where an arrow hints to go down, while the hidden door is actually above.
When a hidden door is entered, it will usually lead into a small room with a turquoise cube, or an orange cube which is harder to reach. Obtaining the items from orange cubes is necessary increase one's clear %.
Only red doors are featured in this mode. They appear randomly across the map, and lead to special rooms where players can attempt a timed challenge for additional power-ups. Sometimes they lead to bonus rooms, with stat boosts, treasure chests, food or Iridescent Glint Beetles available without the need of a trial.