The Cells are a dungeon area located next to the Nave. It is inaccessible from the Nave upon first arriving, and likewise cannot be entered after it is left.
After collecting all six orb fragments, Daniel is captured by three Servant Grunts upon attempting to pass through the Chancel. The Gatherers bring him to the Cells, where he is locked in. After Alexander mocks Daniel, he must free himself before the Shadow has the chance to kill him, and then escape from the area with the guardian in hot pursuit.
There is also a way to end the game here; if Daniel stays in the cell and does not escape, the Shadow will overtake the cell and consume Daniel. Alexander will thank the player and the ending will progress in an identical manner to Alexander's ending in the Orb Chamber.
- There are two ways to escape the cell; you can remove a weak part of the cell bars and use it (or the hammer and chipper) to open a small hole in the brick wall which you can break down to escape. You can also drag the bed to the cell bars, remove the weak part of the cell bar and jump-crouch through it to get out.
- There are also two ways to get the key. You can either get the bucket of water to flush out the key of the pipe, or you can use the cell bar part on the pipe to get the key.
- It was originally planned that Daniel would be captured and escape from the Shadow in the Crypt instead of the Cells. This was dropped from the final version of the game; however, Frictional Games later used the Crypt for Amnesia's expansion pack Justine.
- The Intelligence of the Grunt can be discussed, since the Grunt left the Cells without destroying the Main Hall exit door, or even hide the Key to escape the Cells.