Apart from those, Hardened Power Armor and a Turbo Plasma Rifle usually does wonders, if you're using energy weapons. Maybe take some combat drugs too. Just one of each though, don't wanna die from the come-down. You can also throw EMP grenades at him. And don't get too close to him, since he's using a burst weapon and that's gonna hurt at close range.
It's been a long time, but can you aim at his guns? Because you can do this with Horrigan in 2 (in fact, it's quite funny to fracture his 4 members, he becomes pathetic)
If you are going to shoot him, there is a pillar in the bottom left of his chamber. Use that to shield yourself from his attacks while taking potshots/killing his reinforcements
Are you shooting him? If so, shoot him some more, and more, and more. He has a lot of HP... Use EMP grenades, a couple of them kills him.
If I remember correctly you need the keycard (or similar item) off the Lieutenant, which you can use on the nuke to activate it.
Why in would you want to kill the master?! You prime normals would be much better off joining the Unity rather than fighting against it. Within the Unity you will be improved, through our Unity, the world will survive.
