Actually it was FEAR 2. And sadly it was the only shocking part of the story - it wasn't the colossal fuckup that FEAR 3 was (both in terms of retcons, making the awful mistake of bringing back a great antagonist who had his full character arc in FEAR 1 and didn't have anywhere interesting left to go (by the time you finally capture him in FEAR 1, you've learnt that he's leading precision strikes on guys who have been doing an experiment that's fucked up beyond words and deserve to die, that you're his brother, and he ends up letting you kill him without fighting back rather than kill his kid brother), and utter craphole of a story) - but it was a massive step down from FEAR 1 (which really didn't need a sequel - they should have cut that crappy sequel-bait last scene, as the scene just before was a perfectly crafted ending).
FEAR 1 SPOILERS BELOW
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Oh, and to answer an earlier question - is there a game where a female character gets successfully raped? FEAR 1. Many many times, from the moment she hit puberty until she had 2 kids and eventually got enough control of her psychic powers that she became too uncontrollable and had to be put in stasis.
Obviously you don't see any of it - you've come to stop Fettel many years afterwards, and whilst it's clear from about 1/3 in that the company was doing something fucked up, it isn't until a fair bit later that you find out just how fucked up it was (and then when you think it couldn't get worse, you find out it was the CEO's own daughter). And then you find out that you and Fettel are her kids and he's got a pretty good reason for what he's doing. It's part of why the initial ending (before the sequel-bait helicopter bit) fits the game so much better - Fettel has done what he was after (he's gotten his revenge on everyone involved in the experiment, freed Alma from stasis, lead his brother to the various evidence of what has happened and who they are, and allowed his brother to kill him), and ironically (given that the thing Alma was most furious about was that they took her kids away from her) when you finally encounter her in her physical/zombie form (rather than her various psychic apparitions) she immediately tries to kill you. If you kill her instead, she realises at the very last gunshot that you're her kid, and the game flashes to a scene of her screaming as the scientists rip the infant protagonist away from her. Much better ending, mood-wise, for a game that in its last third became much more of a 'depressingly fucked up horror' than a 'monster closet horror' (the helicopter sequel-bait is very much in the 'monster closet' category and out of whack with the mood of the game by that point).
To be fair, FEAR 2 had some potential - you get a good explanation of why (after the 1st mission) the protagonist gets the same ability as the point man in FEAR 1, and the idea of the company copying the genetics of both the protagonist and Fettel from FEAR 1 and using it to psychicaly 'augment' a whole team of soldiers against their will/knowledge could have been interesting. But if they were going to play that card, they really needed a LOT more character development and time spent with the other squadmates (especially the one you end up fighting), to stop it from being just a cheesy way of explaining why someone other than the FEAR 1 protagonist has the same super-speed and psychic link to Alma. For that matter, it was a bit retarded that all the squadmates seemed to have the protagonist's powers - it's clear in FEAR 1 that whilst both brothers have the psychic link, their powers are completely different and there's a random element to what powers will manifest (the protagonist has his super-speed, Fettel can psychically control a small army of clones and reads the memories of the guys he is killing by eating their brains): it was fine to have a boss-fight against a soldier with identical powers to you, but the sections where you're travelling with the other soliders who survived the augmentation process could have been much more tactical if they had different powers to you, enabling you to work as a team.