The NPC next to the player is the ally, they must follow the player.
The three NPC's next to the fake door in the second room are to spawn when the player triggers the trigger zone.
The NPC on the walkway, second floor is there to test shooting down at the player.
The third room has an NPC right next to the door that if possible to do, is meant to grapple the player, the player should in some way fight off this melee attacking NPC that has grabbed hold of them.
Leave the NPC around the corner of the third room alone, run up the stairs and kill the 2 NPCs there. The three NPC's should spawn as you have now triggered the trigger zone (when I tested this, they never spawned, though all the settings seemed correct). Kill the NPCS that should follow the player from the other room.
Now the NPC you left around the corner, look down on him, test to see if he shoots you. He didn't shoot at me when I tested.
The ally the player has should walk to the door that is remote operated and start working on it, some how, after a short while he should manage to open the door.
The player then needs to go into the room and and kill the BOSS Conker to win, "end the level".
DOWNLOAD:
http://danielhiggins.co.uk/files/test_001.fpm
Contact me if you need any more information.
//EDIT
I updated the map so that the spawned enemies actally spawn and follow the waypoint into the room.
Windows 7 Home Premium 64-bit, AMD Phenom II X4 940 3.0Ghz, 2.0GB Single-Channel DDR2 @ 400MHz, ATI Radeon Sapphire HD 5770 Vapor-X