1. Descend the stairs into the Catacombs. Somewhere down here is Silhouette's hideout.
2. Keep left then descend the ladder through this crawlspace. Alternately, stay right and grab the Gas Grenade fixed to the wall before descending through here. You'll find a lockpick and a Napalm Canister below.
3. Follow the crawlspace. Before exiting use a Gas Grenade and Tranquilizer Darts to bring down these two MJ12. Remember to stay in the crawlspace for protection until they're incapacitated. The nearby crate holds 12 Gauge Buckshot Shells. Ascend the ramp. If you turn right at the top of the ramp you can disable the Gas Grenade, otherwise continue left.
4. Tracer Tong is your docent, explaining the history of the Catacombs.
5. Every patrol you encounter must be incapacitated, for reasons that will become clear in a bit.
6. When you get to this junction, you'll see this MJ12 Commando patrolling a series of stacks similar to a library. You can proceed directly to the left or head around to the right for a crawlspace that will bring you out to the opening just visible behind the Commando.
7. Many abandon pacifist play when it comes to the MJ12 Commandos, opting instead to blow them to kingdom come with LAMs. There is an easy way for pacifists to go Commando. A single jolt with your Prod in the lower back as seen here, right where the "shirt" meets the "pants" will do the job. You must be precise, however, as this sweet spot is very narrow. It helps to shadow the Commando until he comes to a stopping point in his patrol routine, then strike with precision.
8. Another incentive to not blow up the Commandos is that each carries a Bioelectric Cell!
9. Continue down this corridor.
10. Push either of the indicated loose bricks, one under a wine bottle, the other under a Lockpick.
11. This secret entrance opens - Silhouette's secret bunker!
12. You earn a Critical Location bonus of 150 skill points. It is wise to close the bunker door with this switch before proceeding.
13. Talk to this child and learn that MJ12 is holding his mother hostage.
14. You'll find Chad, Silhouette's leader, through here. You earn a Subject Acquisition Bonus of 250 skill points.
15. Talk to Chad and he'll give you the blast door key and a map.
16. Don't waste a Lockpick on this cabinet. Inside is another copy of the blast door key and Shakespeare's Richard III. Do, however, grab the Medkit above.
17. Exit the bunker and unlock the blast door. You can proceed left or right, both tunnels converge.
18. An MJ12 Commando patrols here. Bring him down using the technique revealed earlier.
19. Pick the lock on this chest for a DataCube revealing the security account HELA/RAGNAROK. Also inside is a Prod Charger and throwing knives.
20. Continue to this bunker on the right.
21. Finally, someone selling something besides ammo, and at reasonable prices. Of course he's a Zyme junkie (there's a vial on the ground nearby). You can buy MedKits for c600 and Tranquilizer Darts for c200.
22. Continue north by staying right at the junction and you'll come to this closed-off area. Disarm then take the LAM on the right. The crates contain 10mm and 30.06 Ammo.
23. Return to this junction, this time turning left.
24. Make another left here as well, where Tong advises that Jock is picking up heat signatures.
25. Head toward the cross you'll see on the right, knocking out this MJ12 Troop. Head left.
26. Bring down this Troop as well before ascending the ladder.
27. Activate your Speed Enhancement and jump on top of the malfunctioning unit. Crouch, and with your Speed Enhancement still activated, hop onto the ledge above.
28. Follow the ledge over the locked gate into the room with the Repair Bot.
29. Push the switch visible here on the left. The doors slide open and the Repair Bot repairs the malfunctioning unit. You are now free to proceed to the other side of the room and grab the supplies. You'll find Tech Goggles and a Multitool in the crates, plus a Napalm Canister on the ground and 20mm HE Ammo on the ledge above.
30. Return to the area with the cross we saw earlier. Note the hallway to Bunker III is blocked by lasers. Bypass them by crawling through the space behind the cross.
31. Tong advises that the hostages are probably nearby. You'll find an opening from the crawlspace on the left, but be careful as MJ12 Troops and Commandos patrol within the bunker. Wait until the coast is clear, then hop into this small pool.
32. Swim all the way across to the end of this tunnel.
33. Quietly pop your head up for a look, but be careful -- a Woman in Black and a Commando patrol here. Your eventual objective is the indicated Security Terminal.
34. This is one of the most difficult moments of the game. Observe the patterns of the WIB and the Commando. Approach one when you are free from observation by the other, the security camera, and any other patrols in the front of the bunker.
35. I found this to be a good spot to Prod the Commando.
36. And this to be a good spot to Prod the WIB. Use the account HELA/RAGNAROK on the Security Terminal to deactivate two cameras.
37. On this table rest two Prod Chargers, the Catacombs Sewer Entry Key, a DataCube with some background, and a Sniper Rifle. The nearby crates hold a Multitool and 12 Gauge Shotgun Shells, plus Tech Goggles.
38. Ascend these stairs, or, alternately, the ladder across the bunker. Drop the Commando with your Prod and search the crates for a Bioelectric Cell and Darts.
39. There are now two Commandos and three MJ12 Troops remaining, all within this circular area. Carefully bring each one down with your Prod, remembering the Prod technique for Commandos.
40. The area is now secure. Use your keyring to open the indicated blast door.
41. Head inside to complete the Secondary Goal and earn 250 skill points. Follow the hostages as they flee the bunker and return to the Silhouette hideout. If you hadn't incapacitated all of the patrols, the hostages would be in danger now.
42. Return to Chad for a cutscene and 500 skill points. Talk to Chad repeatedly for a seemingly endless litany of political paranoia.
43. Return to the juncture we encountered earlier, but this time keep right. Use your Catacombs Sewer Entry Key on this door. You earn 50 skill points.
44. Descend the stairs, then grab the Lockpick out of this small pool.
45. Continue down the corridor. There are no junctions so you can't get lost.
46. You'll eventually come to this ladder. Descend to load the next level.