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You've contacted Morgan Everett in Chateau DuClare and now you're attempting to give him information about the Gray Death virus, on a computer within the Knights Templar Cathedral in Paris. From the DuClare crypt, head through the sewers to reach a ladder. Climb up to enter a small area with stackable crates, giving access to a nearby window. Climb up, break the window and enter the dilapidated room with fallen beam leading up to the second story.
Climb the beam to the second floor and take the gatekeeper's nanokey in the corner. If you wanted, you could break a window and shimmy across the window ledges beyond the gate and drop down, but it's easier this way. Head back out through the window downstairs and around to the gate. Unlock it using the key but beware an MJ12 commando (at about where the map says "Begin") patrolling the area beyond. Take him out while sneaking or from afar, it's your choice, and then proceed a little further to see a bridge beyond. On the map, it's marked Guard Bridge. Beware three MJ12 troopers on the bridge waiting for a sniping opportunity. Fortunately there are plenty of niches and stone markers in the center of the street to hide behind.
Just beyond the bridge a military robot patrols. We'll take him out of the picture but for now be careful. Approach under the bridge, taking the guards out by sniping first if you prefer. Below the bridge on the left is a small window with goods inside, alarm and camera. First, avoid the robot and pick the door under the bridge, opposite the window. Ascend, take out the guards and cross the bridge. Use the security computer terminal on the other side to deactivate the robot. Take the stairs back down and break open the window if you want. No troops will come now.
Head up the street to the niche that says "Metro Entrance". An MJ12 and commando patrol around this entrance. You can avoid them easily by sneaking by. We'll be coming back to the Metro later so pass it up for now. Ahead, there's another MJ12 who patrols up and down this passage. Take it and hide behind one of the stone pillars in the niche to the left or right until he passes, and do what you please with him. Your objective is to get to the cathedral area. Pass over the bridge with water underneath (which is another entrance, but an unecessary risk and likely to cause undue attention when you emerge at the place marked "old well") and pause when you get to the cathedral opening. There are several MJ12 troops and bots walking around.
Your goal is to make it to the place marked #1 on the map, a scalable trellis near the Monk's Quarters entrance. If you watch their patterns you can easily sneak to the trellis and climb up. There's a bot patrolling nearby the trellis and a crate with rare 30.06 ammo that you may want to break open near its base. Climb up and you'll be on the roof. Gunther will soon chime in with a message, so climb up the flying buttress to the next higher section of roof and then move over to the left so you can have a view at the window where #2 is. There's a troop looking out so snipe or tranq him first, and then jump onto the flying buttress near the window, and then climb up that to the next higher level. Walk around to the bridge and look out for MJ12 snipers. Before you cross, consider exploring this side of the cathedral, both upstairs and down near the monks' quarters for a few extra items, nothing really substantial.
Cross the bridge to the #3 building and head down the flight of stairs until you reach the first archway (-further down is the kitchen but only go there if you feel like exploring). One piece of advice. If you plan on fighting Gunther instead of using his killphrase (if you indeed have it from Paris), keep an eye out for a couple fire extinguishers, as he favors flamethrowers. Enter and proceed down two more flights of stairs. At the bottom there will be a small hallway with a locked door to the left (with the gold you're supposed to find), and another stairway up on the other side. Skip the door for now, climb the stairway and you'll be able to go left or right. Right will lead you to a small room with camera, MJ12 troop and turret, and your main goal eventually, but left is where we want for now. Head left at the top of the stairs, go up some more stairs and you'll hit two doors: one on the left and another on the right. The left is locked and just leads outside (past another locked door). The right unlocked door is what we want. Inside is a WIB (woman in black) so be careful.
Take her down, and search the datacube on the table for a list of all needed passcodes (1942 for the vault, 0022 for wisdom and 34501/08711 for security), and a nanokey for the main entrance. Behind the wall in the back is a security computer terminal. Use it with the code "34501" and "08711" and disable the camera in the computer room.
Head back downstairs, and down again to the locked door on the right this time. Enter 1942 and enter. Drop down and disable the laser field via the electronic panel. Ahead is the gold cache for your secondary goal. There are two cameras in the room and some nice supplies to be found. There's also a handy security computer terminal on the back wall. Make a run for the back wall, ignoring the turrets (or simply take out the cameras with sniper rifle). Once there you'll be safe from camera and turret. Hack it to disable them and then search around for supplies. Time to deal with Gunther.
Head out of the vault, take a left and up the stairs. This time, take the right passage down into a small room, but hold up before you get there. An MJ12 troop, if he didn't already come out, will still be there. So is a camera on the far wall and another turret. Simply take out the camera with sniper rifle or toss a LAM. Go to the door and use the 0022 code you received from the WIB's room (or elsewhere if you explored). Enter into a room with a ladder. Follow it to gain some bonus exploration skill points, then head back down and around until you shortly see the main computer room. A few choices await.
Gunther is in this room... and waiting. Where? He's just to the right of the staircase but near the wall. As soon as he sees you he's going to start running toward you to initiate conversation. It will go something like this:
Gunther: Hey there.
Gunther: Prepare to be destroyed.
possible option a) You (if you saw Jaime Reyes in Paris and got his killphrase): I don't think so: "laputan machine". [and Gunther explodes]
always an option b) You (if you never spoke to Reyes in Paris, but instead saw him in Hong Kong): Can't some sort of agreement be reached?
Gunther (if b): No. Now you die. [he attacks with flamethrower]
Whether or not you have his killphrase you can decide to kill him by allowing him to come to you first, or you can take the first strike and he'll only use his gun. Get your favorite weapon ready (in my case, the sniper rifle) and instead of turning right at the bottom of the stairs, go straight and a little left so that Gunther doesn't see you. Sneak around a pillar and prepare your weapon. Face toward where Gunther should be and edge out. Immediately fire shots to the head if using the sniper rifle, or blow him to pieces with your favorite weapon. If he's fired upon first, he'll take out his gun and start shooting back. However, if you wait until after the conversation he's going to use his flamethrower and either you're going to want some regen capability or fire extinguishers. I could take him down in two shots to the head with the sniper rifle and not even a scratch... he's not really very tough.
When the Gunther episode reaches a conclusion, walk over to the computer and logon with "34501" and "08711", and establish the system uplink, transferring what is known about the gray death virus to Morgan Everett. He'll chime in that a meeting should take place and tell you to come to the subway at the Metro Station. On your way out, be sure to talk with the Walton Simons hologram that's now at the far end of the room. When finished, head back the way you came, all the way to the first archway you entered from crossing the bridge. Instead of going up though, head down to the ground level and out the front door, using the nanokey you got from the WIB room to unlock it. Turn on speed and make a sprint for the Metro station you passed much earlier.
Take the stairs and the door you'll want to go through after you explore is to the south. There's a repair bot in one of the rooms, and a techie equipment seller in another, with an explorable bonus just above him. Head through the south exit when finished and follow it to the subway. Atanwe at the far end will come running to you and have a chat. No matter your response, you'll be drugged and taken to the home of Morgan Everett.