The first time, he charges your base directly, while the second time, he'll attack the boulder keeps you have (or your base again if they are in his control). The boss, Darunia, can be fought up to three times over the course of the battle.
Capturing these keeps does not stop the rock attacks for good: if they get recaptured later, they'll go right back to bombarding your base. Your base is under constant attack right from the start, including from two rock-bombarding keeps that are around the middle of the map.
