You'll emerge in these tunnels near your objective: the Knights Templar Cathedral. Follow the sewer to this ladder. Morgan Everett gives you a map of the cathedral.
Climb these crates, smash the window and enter the building.
Grab the c100 on the body and the c150 in the corner. Climb this beam to the upper floor.
In this nook is a Lockpick and the Gatekeeper's key.
Exit the building the way you came and unlock this gate with the Gatekeeper's key.
Knock out the Commando using the technique revealed earlier.
Beware the patrol atop this bridge and head over to the indicated area.
Bypass the Alarm Sounder Panel with a Multitool. Smash the glass with a Baton or Crowbar. Quickly deactivate the alarm.
Hack the Security Panel to turn off the camera. Grab whatever you want among the Tranquilizer Darts, Flare Darts, Sniper Rifle and Mini-Crossbow.
Use a LAM or Lockpicks to break into this door.
Use your Prod to take down the three MJ12 Troops on the bridge. Check the bodies for supplies, including two LAMs.
Cross the bridge and smash these two crates for a Lockpick and a Multitool. Grab the credit chit for c100 (visible on the left ledge).
Hack the Security Terminal on the right to shutdown the MilBot Patrol Unit below.
Return to the street. Ignore the Metro station on the left, instead continuing as indicated. If you like, you can risk busting open the crate to the right of the station entrance for Ballistic Armor.
The bridge ahead is patrolled by MJ12. When the coast is clear, proceed to the bridge then leap into the water below.
Swim through the opening ahead.
Be mindful of your air supply as there are no air pockets in this area. Bust open this floating Supply Crate for a Lockpick, then proceed through the next opening.
Carefully emerge from the water -- there are MJ12 patrolling the immediate area.
Proceed northeast, shadowing the bots patrolling the back of the cathedral.
Carefully approach the indicated trellis. The crates to the left hold 30.06 Ammo and Napalm.
Proceed up the buttress as indicated.
Once on the roof you receive a threatening message from Gunther -- he sees you. Smash the skylight to enter the cathedral. If your Speed Enhancement is at Tech Four, you can make the jump to the adjoining terrace seen here. Try it for fun.
You drop into the library. Grab the Cathedral Main Door key here.
Two MJ12 Commandos patrol downstairs. Bring them down with your Prod as revealed earlier.
This DataCube reveals the Sidon's Vault key 1942, the Fountain of Wisdom key 0022, plus the Number 34501 and Secret 08711. By the foot of the bed is a Recoil Weapon Mod. In the neighboring rooms you'll find two credit chits worth a total of c350, plus another Cathedral Main Door key.
Return up the stairs and pass the library. If you're low on Prod Charges like I am here, use a combination of Gas and several Tranquilizer Darts to bring down the MJ12 Troop at this position. Continue up the stairs.
You need to cross this bridge to the other tower. Prods are the easiest way to bring town the Troops, but Gas/Tranq Darts will do the trick. Just be sure to maintain cover as the Troops can fire back while disoriented.
Descend all the way to the bottom of the stairs.
You emerge in the kitchen. Talk to the chef and he'll give you directions to the computer room, sort of. What you'll find in your Notes doesn't quite match what he says. Grab the fire extinguisher if you don't plan on using Gunther's killphrase.
Return up the stairs, make the first left, head down more stairs, then enter the code 1942 on this door to the left
You earn an Area Location Bonus of 250 skill points. Bypass this Control Panel to disable the lasers beyond.
You've found Everett's gold. Immediately proceed to the rear of the room where indicated.
Enter the account 34501/08711 into the indicated Security Terminal to disable three security cameras. Recharge at the Repair Bot.
Search the area for Reload and Scope Weapon Mods, a LAW, Rockets, and this Bioelectric Cell and Range Weapon Mod up here.
Return to the stairs. Head all the way up, keeping left, then approach this unlocked door on the right. (The locked door on the left holds Darts and Flare Darts - which can be accessed for free later.)
Inside is a Woman in Black. Gas Grenades and Tranquilizer Darts will bring her down, just be sure to maintain cover. Close the door behind yourself to muffle the sound of her return fire.
Under the table is another Fire Extinguisher. On the table is a DataCube with the same information found earlier, plus another Cathedral Main Door key. A Stealth Pistol is on the night table, and a locked cabinet holds c400, 12 Gauge Buckshot Shells and Throwing Knives - not worth the Lockpicks IMHO.
Use the account 34501/08711 on this Security Terminal to disable one security camera. Take the Dragon's Tooth Sword off the WIB if you plan on fighting Gunther.
Return down the stairs, this time passing through this doorway on the left.
Knock out the Troop, then use an EMP Grenade or your Spy Drone to disable the camera in the far corner. Enter the code 0022 into the keypad.
The crate ahead holds another Fire Extinguisher.
The ladder leads to an Exploration Bonus of 150 skill points and the Darts we bypassed earlier. If the secret door closes behind you, it can be reopened by moving the lamp on the door next to it, on the north wall. (Thanks for the tip, Shido534.) When you're ready to confront Gunther, return down the ladder and head down the stairs.
Time for some choices. Gunther is waiting here. If you don't want to kill him, it's wise to rush to the computer beneath the cross before he reaches you.
You'll earn a Critical Location Bonus of 500 skill points. Login with the account 34501/08711 and select "Establish System Uplink" to complete the primary objective.
Gunther finally speaks once he approaches. If you spoke with Jaime in the cafe, you'll have the dialogue option, "I know your UNATCO killphrase: Laputan machine."
If you use the killphrase, Gunther explodes, after protesting, "I -- am not -- a -- machi --"
Of course, if you're going for minimum-kills, or you just like a fair fight, you'll pick the dialogue option, "...How about we make a gentlemen's agreement?" Gunther is no gentlemen, and he promptly unloads his flamethrower on you. Good thing you have all those fire extinguishers. (1) (2) (3) Note the hologram ahead.
The hologram is viewable only after Gunther is defeated, so if you plan on running from Gunther you'll miss this. Simons threatens to send someone after you who is more capable than Gunther. Someone with your abilities.
If you intend to fight Gunther, the Dragon's Tooth Sword from the WIB works well.
My preference is to run from Gunther and keep him alive. Morgan Everett agrees to meet with you and instructs you to head for the subway station you bypassed earlier. Leave the cathedral any way you like -- my choice is to head up the nearby stairs and exit through the indicated window, using Speed Enhancement to break the fall.
Return across the bridge this time -- swimming is possible but it's very tough to get out of the water. Icarus complains that you are bringing the Illuminati closer to power.
Morgan Everett informs you that Icarus is the voice of a Majestic 12 AI. Everett claims he can protect you and Daedalus for a day or so. The crate on the right holds Ballistic Armor.
Next, Bob Page radios. You've accumulated quite an audience. Continue into the Metro and Everett instructs you to meet his associate, Toby Atanwe, below.
Enter the station. To the left is a locked glass door that can be shattered with a LAM or the Dragon's Tooth Sword (thanks, Lance). Inside is this Repair Bot and an ATM.
The door straight ahead leads to this technician who will sell you equipment. A Multitool can be found in a crate on the ledge behind him. A nearby book reveals the partial ATM account "576001/wyrdred0-". Lance suggests replacing the dash with the number "8" to complete the login.
To the right is the door to the tracks below, and Toby Atanwe.
Atanwe approaches, and you are given a dialogue option. Both options result in the same result: you are drugged and taken to Morgan Everett's home.