The clerestory is the line of windows letting in light above the Nave.
Look carefully at the stone ledges running below the clerestory windows. During the civil war a group of parliamentarian soldiers on their way to Crowland in 1643 broke into Moulton Church and shot out the stained glass in the clerestory windows. The ledge was badly damaged by musket balls on the south side, but not so much on the north side. There are also musket ball marks high on the wall in the lady chapel.
