Beating Nemesis
Use the mini-uzi-like gun on Nemesis. It has a faster fire rate and more ammo capacity. Dodge his lightning attacks and shoot Nemesis when he is vulnerable. Throw the glaive at the electricity when he is charging his lightning attack; this should obliterate his shield so you can attack him.
Beating the Stalker
Let Stalker charge you, and when he rolls out of the way, unload the best ammo you have into him. Double shot and fire power are recommended. Be prepared for Stalker's bomb attacks once he climbs up the pillar. He will become visible before he shoots them at you, and his feet will have a green glow. Watch for that glow and attack the shield to blow the bombs back at him. He'll be defeated quickly.
The Final Boss
Use the same weapons that you used to beat Nemesis in this fight. When the tentacles come out of his body, hit the green bubbles with the glaive or shoot them. As they open up, throw the glaive at the electric rod at the top and the middle of the arm where it opened up. When you have attacked all of the arms, throw the glaive at the man inside. Make sure you have electricity on, and control the glaive by pressing "RB" after you throw it. Repeat this process three times to defeat the final boss.
Brutal Mode
Complete ten chapters to unlock Brutal Mode. This is for experts only -- in this mode, you will lose more health and enemies will be more aggressive and more resistant to your attacks. They will reload and fire at different times, which makes it much harder to come out of cover to return fire. This mode can be an entertaining challenge after you've beaten the game on the regular difficulty level.