What you thought you did: Survived by your wits and physical prowess in a desperate escape attempt from a monster-infested utopia gone mad.
What you actually did: Single-mindedly carried out the murderous orders of anyone who used the key phrase “would you kindly,” because that’s all you know how to do. This included killing your own father, crashing a passenger-filled airliner and even snapping a puppy’s neck.
Wait, what!? One thing is certain in the underwater city of Rapture: you’re always in danger from a host of mutant freaks, and you’re not wrong to fight them. Your reasons for fighting them, on the other hand, are a lot more sinister than even you realize until about midway through the game. Guided by an unseen engineer named Atlas, you try to escape from the madhouse, only to watch as Atlas’ family – and your ticket home – are blown up. Only by finding and eliminating Andrew Ryan, the madman at the heart of Rapture, can you hope to ever make it out alive. Or so you’re told.
Of course, there’s more to it than that. Much more. Hints begin to arise when you learn that the Vita-Chambers – which conveniently resurrect you after every death – are keyed to Ryan’s genetic code. Eventually, you learn that you’re nothing less than Ryan’s illegitimate son, spirited away by his enemies and conditioned to unquestioningly obey any command that includes the phrase “would you kindly.”
That phrase has forced you to do horrible things. For starters, you brought down a plane full of people, murdering everyone on board just so you could find the entrance to Rapture. In one recording, you can listen to yourself, as a child, killing a puppy on the orders of a scientist. And when you finally encounter Ryan, he uses it to force you to kill him. Maybe he’s trying to free you when he repeatedly screams, “A man chooses, a slave obeys!” But it doesn’t really matter, because all he gets for his trouble is a putter wedged through his skull.
Once Ryan’s dead, you find out that the “Atlas” who’s been manipulating you this whole time is actually a mob boss named Fontaine, and you’ve just given him complete control over Rapture. You’ve been nothing but a criminal’s tool the whole time, although a narrow escape and a little deprogramming will give you the chance to set things right. Sort of. Maybe.
What you thought you did: Fought to bring down a despicable group of terrorists who’d stolen the cure for a global pandemic known as the Gray Death.
What you actually did: Acted as a tool in the world-domination plot of a super-shadowy organization called Majestic-12.
Wait, what!? In the early stages of Deus Ex, you’re simply JC Denton, a government agent working for the UN Anti-Terrorism Coalition (UNATCO) and trying to track down a shipment of medicine stolen by a secessionist terrorist group called the NFS. As you shoot, stealth and probably just generally murder your way through legions of NFS militiamen, however, it gradually becomes obvious that your enemies aren’t quite as vicious as their reputation, and that your superiors are hiding something from you.
Things come to a head when you’re confronted by JC’s brother Paul, a fellow agent who reveals that he’s been working with the “terrorists” as a double agent the entire time. Furthermore, he reveals that the NFS goons actually have humanity’s interest at heart, and that UNATCO is a front for something far more sinister.
Specifically, the agency’s secretly under the control of Majestic-12, which is also partly responsible for creating and unleashing the Gray Death in a bid to destabilize the world and make it receptive to the idea of a one-world government. It’s the usual conspiracy nonsense we’re used to hearing in the real world, but it’s then backed up by the secessionists’ leader. If you can keep him out of the terrifying metal clutches of your cyborg superior officer, he’ll reveal that you’re actually a clone, created by UNATCO to unknowingly advance Majestic-12’s agenda.
JC’s not sure if he believes any of it, until UNATCO retaliates against Paul’s defection by activating a genetic “kill switch” that’ll leave him dead in 24 hours. As he races to save Paul, he’s told about a secret Majestic-12 facility under UNATCO headquarters – and after he’s arrested and wakes up in a cell within it, he’s got all the proof he needs.
Admittedly, things don’t look too rosy for our nanomachine-augmented turncoat friend, but the events that follow will give him a chance to not only smack down Majestic-12 but possibly take over the world himself, so don’t feel too bad for him.