Activate Speed Enhancement and dash past Bob’s bubble to the door opposite. You can use ballistic armour or thermoptic camo to avoid taking damage.
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Ascend the short ladder, and then into the nearby grate.
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Go all the way down a long ladder and through a vent at the bottom. The datacube has the credentials for the Aquinas Substation and router (used in the Helios ending. Activate your cloak before opening the door. Right outside the door drop open another grate and drop into the vent.
At the other end use the button on the wall to open the floor entry.
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The opening in the floor drops into a flooded pipe. Follow it along until you reach this point. If you look backwards you’ll see a ladder. Quietly surface for air—a commando patrols beyond the fence. If you’re up for a long dive, you’ll find a body beneath the pipes at the bottom of the shaft with a biocell and a multitool, plus a nearby datacube with a disturbing story.
Climb the ladder (cloaking if necessary) and sneak to the other end of the room past the large pipe in the middle. Note that a guard patrols the gantry above the room, too.
Here you’ll find a console with a button to flush the system. Helios radios in to warn you off. Push the button to drain the coolant fluid in preparation for blowing up Area 51. You will see the coolant in the large pipe drain away. When it’s done, Tong radios in and instructs you to return to the reactor room in Sector 3. Bob Page begs you not to go through with it, and offers you Europe in exchange for not going through with the plan.
If you’ve got plenty of biocells you can slip (cloaked) down the steps on the left of the console to find crates with a medikit and a LAW, although smaashing the crates will definitely alert these 2. You can also explore beyond them through a pipe to a hidden area, and up a ladder for more goodies. When you’re ready to leave, activate your cloak and follow the patrolling commando on the upper level.
Note that another guard patrols the gantry above this room too. There are another crate down here (this shot is facing back the way you came) and a metal cabinet with (among other things) a biocell, but again smashing them will cause a commotion.
A body behind the console to the left of the door has a lockpick. Another body on top of the yellow machine has a multitool and a biocell. The ladder of the right of the door leads to the gantry above if you want to brave the troopers for more goodies. You can eventually end up back here, which will probably cost you more biocells than you’ll find! From this position, press the button to open the door. Tong radios in with a reminder of what you’re about to do, and Page makes clear what the consequences will be. A second door beyond this one also opens with a button. Make sure you’re cloaked before opening it.
Still cloaked, exit the door and turn right—recharge at the repair bot if you can.
Head East back to this door near the vent. Head in and climb back up the ladder to the top level.
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At the top, return to Bob Page’s little bubble. Engage Speed Enhancement to dash past the turret and go left (West) through the door you first entered the area.
Through the door turn left up this corridor (avoiding the grays' area to the right). A button to the right of the door opens it.
Back in the cloning lab heal at the medical bot, then through the West door back to Sector 3. Morgan Everett calls in to beg you to go back to kill Bob Page.
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Retrace your steps up the stairs, and up the ladder next to the sign for the Aquinas Hub. Go left at the top to return to Station 17, then down the stairs there to the bottom.
Evade any remaining transgenics through the door at the bottom, and head right to the reactor room.
Inside, Tong radios in to say you need to deactivate the failsafes at the base of each reactor. Time to don a hazmat suit and activate Cloak to evade the grays that roam the area.
Drop down into the hazardous reactor to find the failsafe switch. A tunnel connects the very bottom level providing easy access between the two. Activate both switches then climb a ladder out. Head to the ladder up to the engineer’s room in the NW corner.
Tong radios in to tell you to trigger all 3 ion injectors and then engage the system. The ion injector switches are on the right of the room, with the 1st one open. The engineer warns you that he’s not happy with your course of action. The others open as you engage them. Before pressing the 3rd button, don a ballistic armour if you have one, and engage the Regeneration augmentation.
When you engage the 3rd injector the mechanic draws a pistol and starts firing. All you need to do is hit the "Engage" switch on the right of the console to trigger the destruction of Area 51.
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The explosions begin as you make a run for it.
The final cutscene rolls showing Bob Page in his final moments. The game ends with this quote.