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1 - Entrance
As you enter, you'll spot a sign pointing you to System Ops (or Fluid Ops, as the map refers to it). Before proceeding, turn right and take out the Laser Turret and Hybrid at the far end of the hallway in order to avoid some pain.
2 - Fluid Ops
The main floor of Fluid Ops is rather vacant, with only a single Hybrid and an Auto-Repair Unit to find, but climb the ladder up to the second level and you'll find a corpse guarded by a Swarm Pod. Defeat the Pod (or run from the Swarm it releases) and then grab the broken Stasis Field Generator and 3 Cyber Modules from the body.
3 - Power Ops
Beware of the Laser Turret on your right and the Security Camera on your left when you enter, as well as potential Hybrid attacks. There's an Audio Log right in front of you on the floor as you enter, and serach the larger office on the right as you enter for an ExperTech(tm) Implant and 15 Nanites in the desk. You'll also find Version 2 Repair Software and a Small Beaker in one of the south office desks. Proceed to the room on the west and climb down one of the ladders to Power Ops Lower Level (4).
4 - Power Ops Lower Level & Interpolar Simulation Unit
Descend the ladders and check the ceiling for some Annelid Pods; take them out from a distance if you can. You'll spot the Interpolar Simulation Unit in the next room - the corpse has a French-Epstein Device and Pistol next to it, and some Standard Bullets plus a Laser Rapier in its pockets. Save your game, and then step toward the Sim Unit.
If you listened to the Audio Log found at the entrance to Power Ops (3), you'll probably anticipate something, but not this... doors at the sides of the room will open, and four Annelid Arachnids will pour out! Jeez, isn't one nasty enough? Employ the gentleman's tactic - running away while shooting wildly - and they'll eventually go down. Return to the Simulation Unit when they're all dead, then insert your Interpolated Simulation Chip, and SHODAN will upload you 15 Cyber Modules. Two down, one to go. Hopefully the last has fewer spiders.
5 - Bedroom & Ambush
You'll find an Audio Log just outside the door. While exploring the room, you'll come under attack by two Hybrids and an Annelid Arachnid. So much for no more spiders. Deal with them and then check the lockers for 20 Nanites and a BrawnBoost(TM) Implant, 15 Nanites, a Speed Booster, and another 10 Nanites.
6 - Upgrade Stations
Look right down the hall before entering to spot a Laser Turret near (7); take it out, then proceed into the room for a full array of Upgrade Stations, as well as a corpse with 3 Cyber Modules.
7 - Shooting Range
Not much here except for the Laser Turret defending the hallway, and some Anti-Personnel Bullets at the back of the gallery.
8 - Bio-Reconstruction Device
Sweet, everlasting life! Activate the Bio-Reconstruction Device, but make sure to take out the Security Camera overlooking it on the left.
9 - Replicator
More goodies await those with the Nanites to spend. Grab the Anti-Personnel Shells on the floor, and use the Replicator if you want Cigarettes, Juice, Rifled Slugs or Psi Hypos. You may also hack the machine for a Recycler
(turns objects into Nanites, extremely useful) and Anti-Personnel Bullets.
10 - Armory
Hack the door panel or use the code 13433 to gain entrance. Inside you'll find a Security Bot
, which is similar to the Maintenance Bots you've fought, but has stronger armor and a deadly laser cannon. Suffice is to say, going up against these guys is not fun, so use any and all armor-piercing or EMP weapons at your disposal. Inside, you'll find a perfect-condition Assault Rifle, and some EMP and Fragmentation Grenades in the back room.
11 - Barracks
Check the back of this room for a Grub Pod to destroy; 3 Cyber Modules await you on the floor as a reward. Search the lockers above the beds for an Audio Log, and packs of 15, 15, 20 and 25 Nanites; be careful near the corpse with the Annelid infestation around it, as several Annelid Grubs will leap out and attack you.
12 - Command Center Entrance
Be careful as you approach the door - a Security Bot, as well as two Hybrids and a Laser Turret wait for you inside. My advice? Run, then take them out as they come down the hall, and take out the Laser Turret on its own. When that's done, you'll find some AP Bullets on the corpse inside the room.
13 - Command Center & Red Cyborg Assassin
You'll find the final Red Cyborg Assassin here, who runs off to the left as you enter. Hold off taking chase for now, and take a few minutes to explore the area.
14 - Wreckage
You'll find this path blocked off, but there's an Audio Log and Medical Kit nearby. Check the broken floor panels for 2 Cyber Modules as well.
15 - Command Center Lower Level
Mind the Security Camera as you near the ramp down. The office to the right is inaccessible for the time being. On the lower level, you'll find a few small offices; one has an incomplete Surgical Unit you'll need an Activation Key for; another has some piles of toxic worms along with a Maintenance Tool and some Rifled Slugs; one more has a dead body with 2 Cyber Modules and an Audio Log nearby; and the last contains a Monkey and Psi Booster.
16 - Brig
There's nothing here on the upper level, so take the elevator down. Two cells are blocked (and the corpses inside are empty), but a third isn't... that is, until you step inside. Several Annelid Grubs will spring out of the corpse and the cell will become barred. Take them out in close quarters, but... how to get out? Look up, and you'll spot a fuse box of some sort; shoot it and it will break, shutting the force field down. Search the corpse for an Unresearched Object (WormBlood Implant).
17 - Red Cyborg Assassin & Linear Simulation Unit
Destroy the Security Camera on your way in. Through the door, you'll find the final Red Cyborg Assassin; for killing him and claiming the Linear Simulation Chip, you'll be given 10 Cyber Modules by SHODAN. Proceed into the next room and you'll find the Linear Simulation Unit surrounded by the remains of Bronson and her squad. Insert the Sim Chip, and you'll be sent another 25 Cyber Modules. Bear witness to the death of Xerxes as SHODAN infiltrates the ship's main data loop. She thanks you in her backhanded sort of way, and then tells you to get to Recreation, Deck 5.
Search one of the corpses for Bronson's final Audio Log, and the desk and lockers for a Maintenance Tool, some Anti-Personnel Shells and Standard Bullets, 40 Nanites, a Psi Hypo and a superb-quality Laser Pistol
. Finally, you're just about done with Ops! Get back to the Elevator in Operations B and ride it up to Recreation. Time for some... rest? Good luck.
18 - Ops Override Office
After getting the Ops Override Access Card from the Bridge on Deck 6, you'll need to come back here; the door will only open for you if you've got the card. Inside, use the terminal on the wall and SHODAN will give you the code 94834, for use in Engineering A. When that's done... yep, it's time for more backtracking. Head back to the elevator and take it down to the Engineering Core area, where you got the ship's engines back online at the beginning of the game.
B - Transition to Operations Sector B
S - Security Control Stations