Yeah, after the initial damage phase when you arrive via the elevator, when he goes up top to the two towers, he shields himself with an impenetrable shield. So some balls will be exposed where a ship comes down and removes some stuff, just like in the beginning portion of the strike, you take the balls and slam them in the appropriate side to break his shield. Then he will come down for another dmg phase. This happens twice. Look out for it in your UI, they show you where the balls spawn and when you pick them up it will also show you where to slam them.