To defeat the big boss, you must be careful to not to step in the side hallways. Run around the pit to avoid the big spider shooting you from behind. To defeat this big spider, you must go collect the four artifacts in the hallways, but you can't get them yet. First, you must stun him.
To stun him, you must shoot him from across the pit. But you must be in the front of a hallway entrance facing him, and he must be in front of a hallway entrance also - if not, he will not be stunned. Once he's stunned, run in the entrance and retrieve the artifact and return to the pit area. Repeat these actions, but this time, you cannot shoot the spider in front of the entrance where you've already picked up an artifact. You must be in front of a new entrance that has an uncollected artifact in it. After collecting the four items, the big meteor will fall from the ceiling into the middle of the pit. At that point, the big boss is vulnerable. Shoot him, but don't get too close or stay to far away from him.
After defeating this boss, look for the ladder next to the entrance and climb to the top. Then, back flip to the ledge behind you that looks like a hand. Jump across to the platform between the two lights, enter the passage, and enter the crawlspace to the end. Jump to the ledge and grab. Jump to the next ledge on the side and climb up to the ground. From here, you must shoot any enemies coming toward you to get to end of the passage to push the switch next to the fence. Enter the gate and kill all the thugs on the way. Then, jump into the helicopter and finish the game.