Marduk sits on top of a little tower. He will shoot a laser out that will damage you while you stand in it, so keep moving. He also calls backup, one at a time, but they'll start to add up so use your shockwave (ground pound).
There are three clamps on each level of his tower you must destroy, each time you destroy all three clamps, the tower descends a level.
Once Marduk is on the ground you need to avoid the falling debris (or just use your healing kits), and avoid his energy ball attack (you'll notice his shield fade as it moves up to his head and turn into a ball that will shoot at you, start moving before it's ready to fire) and keep firing until he is dead.