I think I used it the first time when I could take his shield away, then I fired at him so he lost a lot of energy, and when you do it correct I think you can stay in Hypermode to weaken him until you can take his shield off a second time and then you can destroy him completely. I only know about normal mode though, and I'm not even sure if I didn't go into Hyper twice to beat him completely.
Anyway, I think it would be a waste to go into Hyper before he lost his shield, but once you are in, you should try to stay in as long as possible.
On another note, I ran into Ghor today and I got to say that he was very easy to defeat. I haven't seen a difficult boss for quite a while now, and I definitely have to say that Prime 3 is the easiest so far.







