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For this first section, use the map labeled "First Part". After you get into the Aquinas Hub area, use the map below it labeled "Second Part." Both parts are connected by a single ladder, labeled "ladder down" and "ladder up" respectively. As you approach Sector 3 proper where it says "Enter" on the map, you're greeted by a holographic Tong, pitching you his version of how events should transpire, which, if completed, would lead to a "new dark ages." In the end, only one ending can be the true ending, but you can choose any one of the three: Everett and the Illuminati, Tong and his New Dark Ages, or Helios and the magical juxtaposition.
Past Tong is Sector 3, a smallish open area spanning several stories yet with a lot to do, and with many guards patrolling all the nooks and crannies - not to mention animals. You'll soon find out via transmission from Helios that you need to get to the Aquinas Hub, which is to your right through the locked door and up the stairs a few flights. However, the code to Aquinas is in the Reactor Lab, the door to which is to right of the stairway shaft (simply follow the signs) in an open area below.
Ahead of you on the left side of the main level are two karkians, a big and small one, and a greasel. Hug the left wall, keeping an eye out for catwalk guards above, and move forward. Just before the pool, if you look right, you'll see the karkians. Head to the ladder at the end of the wall at #1. Climb it quickly before you are spotted by the greasel, or else simply take it out before hand, as it's likely nearby. Once on top you'll be safe from guards and animals alike on a dark stretch of catwalk. From here I find it easy to either pick off the karkians below with a silent weapon or start taking on the guards.
Look down from the catwalk into the green pool labeled "Coolant Filtration", where two greasels are swimming. Take them out first from above, then crouch/dive into the pool, finding the nanokey to the stairway door, and also a datacube floating on the surface with the Reactor Lab key code, 2001 (also Alex J's door code back at UNATCO).
Swim through the opening in the pool back to a stairway and take it up through the door. Hopefully the animals were destroyed from above, but if not, Cloak past or take them out here. To your left after you exit the small door facing the green pool is the staircase. Immediately around the corner nearby to your left is the Reactor Lab door below at #2... and a couple of spiders. I really dislike these spiders. However, you don't have to deal with them. Instead of taking the stairs down, walk toward the door from the upper level just above the spiders. Jump down, enter the 2001 keycode, and enter quickly.
Here's possibly your second taste of aliens, this time alive. Ahead is a green gaseous room with a couple of live grey aliens, which actually do considerable ranged damage with their radioactive spit. They die like human beings though, so if one sees you and attacks, use your normal defenses. Or Cloak. Head across the bridge over the reactors, take a short right and into the door on your left. Climb the ladder to a mechanic at #3 (which incidentally is where you'll also be coming if you choose the New Dark Ages ending), who will give you the Aquinas Hub code, 1038. Backtrack to the flight of stairs at #4 and use your key from the green pool if it's not already opened by alerted guards.
Walk up past the Aquinas Hub door to Station 17, and enter. You'll find a mechanic and augmentation upgrade canister behind safety glass. To its left is a ladder down (with sniper and nice 30.06 ammo) and another door at its end. Through the door is likely another guard, either here or out on the catwalk through the door on the other end of the small room. Read the datacube on the desk for the security code: "area51" and "bravo13". Up the short ladder in this room you'll find a darkened roof with a datacube near a dead body, giving you a storage code, 4225.
Use the "area51" and "bravo13" login on the security computer terminal near the augmentation upgrade canister to open it and, if you want, open or close the Reactor Lab door which we've already been through. Take stairs back down to Aquinas Hub and enter the 1038 code on the keypad. Enter into a large windowed room at #5 overlooking a big drop below and a stairway to the right if you look out. Below you can see a giant spider on the ground (also labeled on the map), and another skywalk to the left, just a little below your current level. To the spider's left is the Sector 4 door, exactly where you want to go.
However, you'll need to speak with Helios first. Before that, while still in the room, break the glass windows and toss an EMP, LAM or two to disable or destroy the giant spider way below, labeled on the map. You can snipe guards from here if you wish, and there's a secret trap door out near the pipes that extend from this room, but we won't take it.
Go to the ladder labeled "ladder down" on the opposite side of the room. You'll receive a couple transmissions from Dowd and Page, and either Cloak here or get your gun ready. Down the ladder is a room with two grey aliens, likely below you but with the ability to roam and possibly see you. They are near where the map says "ladder up" on the Second Part. If one does see you, it will follow the small stairway up and can take you down in two shots with its range radiation attack. Get it before it gets you. You may as well take out the other one as well, unless you decide to cloak. Whatever your choice, head up the small stairs near the ladder bottom to a corridor patrolled by an MJ12 commando. Take him out or sneak by, and descend a couple sets of stairs to #6. Take one more set of stairs down on either the right or left (both leading to the same place), and go to the lift at the end of the room.
Take the lift to level 3 and talk with Helios at the end of the catwalk, at #7. He'll propose his ending, that you merge with him to create a just benevolent rulership over the world. Interesting, and also my first choice, but once we get to Sector 4 it will be your choice and you can select your ending. Take the lift back down to level 2, and proceed out until you see the security bots at #6 deployed right before the staircase out. Several MJ12 commandos will come running down the staircase and the security bots will destroy them. If the commandos see you, they'll fire at you instead, so back up down the previous staircase until it's over. Then head back up the stairs, through the corridor, down the small stairway into the grey alien room, and notice below, where the aliens were, a datacube next to a dead body. It provides the image for Sector 4.
Outside of that room there's a sniper walking along the stairway if you didn't already take him out. Head down the stairs and you can use your 4225 code on the locked door keypad labeled "Storage A12" for some rockets if you wish. Take the stairs down further, enter the doorway and descend the final stairs down. At the bottom in the darkness is a greasel and a couple of crates. You can avoid them if you want. Walk out into the ground floor with the previously disabled or destroyed giant spider was and with the large door to Sector 4 ahead of you.
As you approach the door at #8, Helios will open it for you. Enter, go up a set of stairs, and through a door via the switch to its side, into a corridor. Open the end door after the loading of Sector 4 and you'll be facing a hologram projector. Walk up to it and Paul or Gary Savage (if Paul is dead) will talk to you about your choices. After the message, head around the circular corridor to another door. Enter a large rectangular room, the actual room of your birth. There are no encounters here save one: an exploding door on the far left end of the room. Head left and watch the door slowly. When it explodes, quickly move back to the right to dodge it, as it flies the length of the huge corridor. Page will chime in.
Read all the datacubes on the birthing chambers, use the medbot if necessary and take the augmentation upgrade canister from the dead scientist's body on the left side of the room. In the middle of the room is a sunken area. Jump or take the stairs down and to the far back underneath the walkway is a dead scientist with datacube. It holds the security login: "lab 12" and "graytest".
Exit the room through the north corridor. [We're off the map now but you'll pick up again shortly when you choose an ending]. After a short distance you'll come to a dark chamber behind glass and door, with a couple gray aliens inside. They could spot you through the glass and charge out of the door so be careful. Use the security computer terminal with the login "lab 12" and "graytest", deactivate the generators in the room, turn off the camera and open the door.
Proceed through the room to the other end, avoiding or taking out the gray aliens as your style permits, and once on the other side, you'll see Page just up the corridor contained in the "Nanotech Infusion Chamber." Taking our your sniper rifle if you have it, walk into the room with page and notice the two turrets on the north and south sides of the room, covered with shields. Walk up to him to initiate his dialogue.
Immediately afterwards the two gun turrets will turn on you. If you're rifle skills are good, you can take each one out with a single sniper bullet. If not, you can always run by if you don't have an appropriate weapon. Remember this. As you run around Page's chamber, you bioelectricity will deplete if you get too close. Always give as wide a berth around page as possible, hugging the walls, and you'll not be harmed.
Now for the endings. You've heard all three pitches: Everett's Illuminati reborn, Tong's New Dark Age, and Helios' plan for merging with you for total control. Save your game here and select one of the three endings from the menu. Each one begins at this point, in the room with page and the, hopefully, destroyed turrets.