The Point Man never going up against Fettel in a direct confrontation in the first game makes a hell of a lot more sense when you consider his abilities as demonstrated in the third. After all, if the Point Man had tried to fight Fettel directly before he surrendered, Fettel would have easily possessed him and blown him up from the inside with about as much difficulty as any other mook. Thus the Point Man is never in a position to fight Fettel directly until he surrenders.
There's a bit of a difference between the Fettel in the first game and the personality of the one in the third. In the first, while he seems to enjoy taunting and playing with the Point Man, he's more focused on finding Alma. In the third, he's actively malicious, taunting, scheming, and generally an evil, laughing prick. But then I realized why when I considered the Creep. It's a manifestation of the memories and ugliest personality traits of Harlan Wade in the minds of three powerful psychics brought about by Alma's uncontrolled powers. Similarly, Paxton Fettel's ghost may very well be the same thing: a manifestation of the ugliest parts of Paxton Fettel's mind, empowered by Alma and his own psychic abilities. If this is the case, the whole thing about Fettel and his grandfather being Not So Different takes on a whole new meaning.
During Beckett's surgery in Project Origin, he keeps blacking out and waking up in a sort of hellish alternate reality where demonic monstrous doctors are operating on him while Alma watches. Exactly why this keeps happening is not made clear....until you read Doctor York's notes on the surgery. Twice during the surgery, Beckett started to die, and both times he suddenly and inexplicably stabilized. And twice during the surgery, we see Beckett blacking out and then see those Alma-demon doctors working on him. In other words, Alma saved Beckett's life twice during the surgery.
On the Vivendi side, there are the Nightcrawlers. They are a very big part of the plot in Persus Mandate, but are completely absent in Extraction Point even where the visited areas overlap, like the subway entrance. Then you consider the timeframe relative to the Origin explosion, and realize that the Sergeant passed these areas much earlier than the Point Man, and enough time has passed by that the Replicas could remove the Nightcrawlers' remains as they set up their staging areas in an apparent effort to occupy Fairport. Meanwhile, the Nightcrawlers have no such purpose: their mission is to collect samples of Alma's and Fettel's DNAs, and since they succeed in retrieving the latter and lose their commander while going after the former, they can just cut their losses and jump off the boat, which is exactly what Raynes' assessment of their MO would imply.
In Project: Origin, the Replica are following Alma's orders and interpreting her desires as their own. Except Alma wants to boink Beckett because she loves him. Which means that the Replica are... ohsweetsacredBuddhawhere'stheBrainBleach....
Alma's physically pregnant and giving birth in F.3.A.R, but as a ghost she doesn't have a womb, so there's no way she could get pregnant. Until you realise that Beckett's female teamate Stokes is trapped in the chamber too, with no indication that she bled out in the 15 seconds between her getting shot and the chamber being closed. And she's nowhere to be seen once you leave the dream...
Very minor but....Armacham didn't let Becket change his clothes for nine months. Those bastards.
It took Yahtzee pointing this out for me to notice, but if you study the covers of the main trilogy, you'll notice that, with each new installment, Alma gets closer and closer and closer to the viewer. *Shudder*
Watch The Alma Interviews, in which Alma mindrapes the Armacham doctor assigned to psychoanalyse her. Then consider this- The monitor in the observation room shows that the cameras are pointed at Dr. Green's desk. The point of the exercise wasn't to see what Alma's mental state was like- it was to see what she'd do to the doctor
Early in the game when you're brought to the T.A.C lab Stokes worries "this thing isn't going to sterilize him or anything is it?" and Aristide replies, "that would be the least of my concerns." Just think, if Beckett had been sterilized we probably wouldn't have F.E.A.R 3.