You must complete the test after you see the weird things.Go on the door with the guard(You will notice that the guard is dead).Then pass through the monsters.If you see the scientist hiding on a trash can(A big one), just leave him there.
When you face the three Tentacles in the test chamber, remember that they only hear you, theyre blind, so dont fire guns.
The best weapon is the grenade, it lures the Tentacle away from you.
When battling Nihilanth, you have to destroy his wall-mounted power sources before aiming at him. A full charged Gauss blast will take it out if youre lucky.
Then concentrate all your firepower on nihilanth. Once you do enough damage, Nihilanth's head wil open and shut.
Equip a fully loaded Shotgun, and jump on an organic trampoline to get above nihilanth.
Fire a couple of secondary fire shells into his brain, and soon enough, Nihilanth falls like a lead balloon.
You need to shoot out his eyes with the two mounted guns. Once theyre busted, get down and rip some serious power into the newly opened cavity. Once the cavity shuts, repeat the process, taking out any Shock Troopers that appear. When the big lunk takes out the bridge, use the barnacle to get across to the second cannon. After a few rounds, Chunky vanishes, leaving you stranded in the helicopter by the G-Man.