On arrival, the base commander will prove to be highly obstructive, only giving ground grudgingly. This attitude will be persuasive through all ranks of the enlisted personnel, and the PC's will be treated with the greatest suspicion. They will deny any involement in the thefts.
At this point the investigators will have to pursue a number of courses, interviewing/interrogating the staff, viewing security camera footage or embarking on some scheme of their own design.
Interrogation will prove fruitless, although under relentless questioning some of the more suspect personnel may break and admit to minor theft and trafficking offenses. But none will confess to the thefts which are the root cause of the investigation.
Reviewing the security camera footage of the warehouse floor reveals no anomalous activity either, and a skilled analysis of the tapes reveals no sign of electronic tampering.
Further, the base command will claim that some the thefts were discovered by their own personnel when loading crates from the elevator to transports in the loading bay. Use of a lie detector machine will back up these claims.
Suspicion should now fall on the elevator shaft connecting the high security subterranean warehouse 6 sub levels down, with the above ground loading bay. An inspection of the elevator shaft reveals that the electronic controls of the elevator have been tampered with, and that an override switch has been fitted, even more interesting will be the discovery of a secret door, carefully camouflaged into the wall of the shaft.
After the door has been forced, the base commander will order an immediate lock down and will dispatch a heavily armed patrol to explore the tunnel, the agents will be ordered by their own superiors to accompany the patrol.
The tunnel descends winding and twisting, ever downwards. Some hundreds of feet in they will encounter a monorail, and this they will be able to follow through immense chambers and galleries of breath taking grandeur.
After what seems many hours they will see a red glow ahead, and hear the faint sounds of hammering. The monorail will take them to a ledge overlooking a vast cavern. On the floor of which, diminished to insect size by immense height of the ledge, hundreds of tiny figures scurry between roaring furnaces and clacking, cranking machines of every type.
At the far end of the cavern an eldritch whirlpool of energies slowly rotates in a swirl of coruscating blue white light.
A shot suddenly sounds from one side, and spinning around the party will see dozens of bizarre looking creatures with dead white hair and bulging blind looking eyes emerge from the darkness. They are armed with a motley array of weapons ranging from medieval crossbows and pole arms to the latest model firearms. And in the background, a thing from a nightmare, with a squid tentacled face and a robe inscribed with hieroglyphic symbols waves them on.