Shooting them in the body didn't seem to work. Go for the limbs, dismember them. That should do the job.
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Hangar 47

1. You will play as Gabe again. After the dialogue, a couple enemies will storm your position. Kill them to begin a Free Look. Gabe will then depart.

2. Weapon Upgrade #1: Look straight up at the ceiling during Free Look and snatch it out of the vent.

3. Text Log #1: After Free Look, Gabe will climb out of the control room, looking to his left. The log will be there, between the console desk and the window.

4. A big brawl against Super Slashers, Slashers, Female Slashers and Leapers will break out. Just keep plowing at them and if you have the Force Gun, shoot them when they get close. If the Females throw acid, throw it back.

5. Gabe and Lexine will back away from a big mob to the other side of the shuttle. Keep shooting; you'll need to take out some monsters coming from nearby vents, as Lexine takes out a Slasher on her own.

6. Ahead is a large horde, some of them Exploders and Pregnants. Try to kill the Exploders from long distance with something like the Line Gun, then grab their pustules and throw them at the Pregnants. There are crates everywhere you can hurl into foes although they can get in the way of item collection if they're scattered around.

7. Weapon Upgrade #2: The INSTANT Gabe starts moving forward after the Exploder battle, keep the pointer on the right side of the screen. Gabe will turn to face Lexine and you will have, literally, a split-second to grab the upgrade, located to the right of Lexine.

8. Audio Log #1: After Weapon Upgrade #2, Gabe will move forward and some more foes will bust out of vents in the ground. Ignore them if you want the Audio Log, which will be behind the pillar to your left. Again, you have literally less than a second to grab it, although Gabe will give you a couple chances to snag it.

9. More Pregnants and other monsters will be ahead. Gabe and Lexine will battle around to the shuttle door and enter it. There's a Contact Beam inside; replace any weapon that's low on ammo with it.

10. Weapon Upgrade #3: Can't miss this as Gabe and Lexine walk around the front of the shuttle.

11. Gabe will need to protect the shuttle while Lexine gets it started. With the Contact Beam, you can pick off all that approach, toasting smaller creatures like Swarms and Leapers with the Flamethrower. Once Nathan shows up, the group will escape and the game will end.

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