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Digitization

 * 1) Page (always after Helios): "Do you see the pieces coming together? UC, AI, and soon Helios will interface directly with my mind. I will be able to see anything, build anything, DO -- anything! Just a little further, Denton..."
 * 2) Where's Everett + why have I heard more from Helios/Page?
 * 3) Page always has "something to say"
 * 4) "A cure! A cure! Do you have any idea how easy it will be to manufacture a new virus? All I have to do is take a very large prime number and multiply ."
 * 5) "Always the optimist. You would need an army to attack me at Area 51, and pretty soon, if the missile is accurate, your "X-51" will be a thin, gray smudge where Vandenburg used to be."
 * 6) Isn't Simons kinda busy? And how'd he get mixed up with Page?
 * 7) "Remember that NSF gentleman I had to dispatch back at UNATCO Headquarters? Guess you were bitten by the same bug. There's no cure, you know, once you have the disease ."
 * 8) "I have a newer version of the firmware."
 * 9) Agents hand-picked? -- gen modified? May explain above...
 * 10) How does Simons have a Dragon's Tooth?
 * 11) Raid on Tong? Explains appearance/sickness
 * 12) Simons as anti-JC -- cool, calm, arrogant, righteous

Missile Silo -- Above Ground

 * 1) Codes altered because of Howard Strong -- Triad name???
 * 2) Troops: "Two words: New York City." "I'm not standing up for Simons. He was careless" "So's Page. He hands over an entire operation to an opportunist like Howard Strong." "I would watch what I say about Bob Page."
 * 3) How do they already know he was dead? Paranoia? Which side? Hidden cameras/microphones?

Analysis

 * 1) Page always comes in after Helios -- he probably uses Helios as a key of some sort to get onto JC's InfoLink, as he either doesn't have the hardware or know-how to do so. And what's the deal with "AI, and soon Helios"? Helios is the AI, unless he means the UC control AI, but that is more of a dynamic algorithm than an AI.
 * 2) Everett has since dropped off the map after JC leaves Paris...he has so little to say when you're on the West Coast but is ecstatic to tell you exactly how to save the world once you get to A51.
 * 3) Childlike mannerisms; Page is the most reactionary character in the game, so it's fitting that he would speak like such a juvenile.
 * 4) ...what? "very large prime number and multiply"? I can't think of anything outside of DNA/RNA sequences that would need a number of such size. However, that disrupts the notion that augmentations and the Gray Death are the same thing (see 7 here).
 * 5) Why wouldn't it be? It's a low-yield nuclear warhead! Could just be the scientist in him talking.
 * 6) Why on earth would Simons risk his own life to take JC out? He has better things to do -- like run the United States, for instance. Simons's backstory is also sketchy at best; he is another candidate for nano-augmentation. This is all we know. He is never mentioned by any major character in connection with the Illuminati. He may simply be a high-ranking government agent that Page determined to be a weak link and a candidate for nano-augmentation. Could he have been bred, like JC? I find that doubtful, due to genetic sampling data found at A51.
 * 7) What disease? Certainly not the Gray Death. Knowledge? Freedom of thought? Insubordination?
 * 8) Newer version...more augmentations? And how is he newer? JC is the newest nano-augged agent among the five operational at the time of the game.
 * 9) Agents may be hand-picked or culled based on certain criterion -- the Yitzhak loyalty scale, for instance.
 * 10) The pace of the sword's mass production is going at a furious clip if Simons already has a sword.
 * 11) Simons may have been present for the raid on Tong's facilities, however, and could simply have picked up the sword along the way or infected Tong.
 * 12) Pretty much; whereas Simons is the opposite of JC morally, Page is the opposite of him in his personality; loud, arrogant, hot-headed.

Missile Silo -- Above Ground
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 * 1) Howard Strong sounds like a triad name -- I was thinking of Gordon Quick, more than likely. Strong is a paranoid mercenary, hired by Page to take care of security at the missile silo.
 * 2) The MJ12 troops are a little slow on the uptake.
 * 3) I'd hazard a guess that they are being monitored at all times, either by higher-ups or Aquinas/Helios. And word of Simons's death travels quickly. JC leaves him in a pool of his own blood a hundred feet under rock and water and the troops already know about it by the time you get to the missile silo (assuming you fly directly there from the Sub-Base). This furthers the idea of complete surveillance. Page, for all of his arrogance, is unsurprisingly paranoid. He's an ex-Illuminati, after all.