Pretty simple boss battle, even though the fella looks scary.
As soon as you finish the cutscene, turn around and you will see a box. Open that up, grab the rail gun. Aim it at Nemesis head, and blast away.
The power from the Rail Gun will now drain. On each side of the room you will see some red canisters. You'll need to push them back into place. But, Nemesis won't let you right away.
You'll need to 'stun' him. Look for the red blobs on his body and make them explode. Any weapon will do, but I used the grenade launcher.
When he is down for the count, hurry and push all those red canisters back into place. If you are lucky, you'll get them done before he gets back up. If not, you'll have to knock him down again.
Once the canisters are back in place, run back to the railgun. Blast Nemesis one more time and BOOM, the fella is dead.