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If you've already read this intro for a different ending, please skip to #1.
A few words about Sector 4. We will begin at the area labeled Page on the UPPER LEVEL. All these end maps (for Helios, Dark Ages and Illuminati) are the same except for the number placement; in other words, all word labels remain consistent. The Sector 4 map may seem confusing at first, but really makes sense as you explore the level and is very accurate. North is up.
There are three levels to the area, the UPPER LEVEL map on top, MID LEVEL map at lower left and LOWER LEVEL map on the right, which I've labeled on the map. You can basically stack each of these levels on top of another, with the central area on each being where Page is.
There are a total of three Universal Constructors on this map, one on every level, labeled in each case: UC-03, UC-02, and UC-01. Each one of these respawns any enemies you kill. On this UPPER LEVEL, there are a pair of spiders roaming the north corridor near the UC. On the MID LEVEL there are a few gray aliens. And on the LOWER LEVEL, there are several karkians and greasels way below. There are no more troops in the game, unless you are backtracking to Sector 3 or choose the New Dark Ages ending. When you're on any level, you are safe from the creatures on any other level.
Fortunately there's a great way to stop their respawning and defeat them as well. On the MID LEVEL and LOWER LEVEL you'll notice I put the labels "Bot". At this point on each level is a security computer terminal that you can hack to release a nearby security bot, which then comes out of its cubby hole and destroys all the beings on the level. It will continue to do so until it's destroyed, protecting you. After you release the bot, it's a great time to go over to the UC door, blow it open with a LAM or use your multitools on the keypad, enter the small room and turn the giant dial, which traps all the spawning creatures on the level, making it safe for you to roam around at your leisure. I strongly recommend doing this on both MID and LOWER levels. The spiders on the upper level will only have to be passed at most once, so no need to worry about the UC up there. Now on with the ending walkthrough.
The Helios ending is the easiest. There are simply three main things to do. Get the code for the Aquinas Substation A3 (labeled on the Lower Level), use the security terminal there and return to the Aquinas Routers on the Upper Level. After you push a few buttons there, return to Helios back in Sector 3 for the end. Now here's the complete run through.
Take the south corridor from Page to #1, climbing a small ladder first. At #1 you'll see an unlocked grate. Open it and take the long ladder down to the lower level. Open a grate down there, crawl into the next room and read the datapad next to the dead body, giving you the key code to the Aquinas Substation A3, 6765.
Climb back up the ladder to #1, and walk onto the lift. Instead of taking it down, crouch and jump (using your Speed Aug to cushion if you have it) onto the nearby roof of the Mid Level at #2. You may if you wish now head west along the roof down to where it says "Bot", hack the security computer terminal to release the security robot, and watch as it destroys any gray aliens on the level. But that may be overkill, as all we really need to do is go to level 3, destroying or Cloaking past any aliens we see.
Drop off the roof you landed on from the lift, and head north to #3 when ready. You'll be overlooking the Lower Level and no doubt see all the creatures below. Just below #3 is the security bot you can release, labeled on the Lower Level map. If you drop and quickly hack the security computer terminal below, you can release the bot and it will destroy all the animals on the Lower Level. Also use the Repair bot down there for a quick recharge. When ready, head over to #4 and use the 6765 code on the keypad to access the Aquinas Substation A3.
As you enter the room at #5 an explosion will happen and the resulting electro static will be deadly. Back away and don a hazmat suit and get your regen ready if you have it. There's also a hazmat suit on a shelf just inside the room to the right. Disable the electronic panel using multitools if you want, or brave the electricity and go to the security computer terminal on the north side of the room, entering the Helios-given login: "page" and "uberalles". Open the Router door and enter the elevator at #6. Take it up to the Upper Level, and walk around to the room at #7, the Aquinas Routers.
Press the engage buttons on the north and south ends, and a computer will open up on the east end of the room. Helios gives you the login for that as well: "icarus" and "panopticon". Use it on the computer to engage the primary router. All that's left now is to meet with Helios "in the flesh." That requires backtracking all the way to Sector 3, ignoring the spiders here on the Upper Level, back out of Sector 4, up the stairs on the west end of level 3, back into the Aquinas Hub where Helios is, up the lift there to level 3, and out on the catwalk to witness one of the three endings of Deus Ex. Congratulations on beating one of the best games of all time!