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Crystal laboratories are underground structures modeled in an ultramodern style. They are easily recognizable due to their crystalline motifs and floating crystals that drop pixels when struck. Sometimes there are floating crystal-like structures above the structure. They are composed of the same material as the base itself.

They are decorated with wall panels, junk tech, and pressurized steel, with Apex and ship doors located inside. Some areas are very dimly lit, with large amounts of lava surrounded in glass illuminating rooms. Interesting structures include a large "control room" with a red metal structure in the center that ejects Matter Blocks when interacted with, it may also kill the player upon interaction. Hi-Tech chests may be rarely found, as well as lava pits and electric traps.

The laboratory is guarded by Apex wearing the Frontliner set of armor (This is a racial set for the Apex, though the guards seem to have a weaker set) that seem "zombified", claiming the player to be an invading non-believer and must die. In some areas, the laboratory may be guarded by Glitch soldiers. Glitch soldiers have the same dialogue and hostility as their Apex counterparts. Enemies have a chance of saying, "They compel me, leave while you can," which may mean they are being coerced or controlled against their will.