A crypt is, basically, the cellar of a church. Some are at ground level, or partially below, with the main body of the church entered by a flight of steps from street level. Others are wholly underground. The word is not used for spaces resulting from archaeological excavations under a church.
Crypts have several uses. Some are subsidiary chapels, or contain several altars for the celebration of private Masses. Some are used for burials. Others are just the repositories of junk and unwanted odds and ends.