Deus Ex/Headscratchers

In the penultimate mission JC launches a nuclear missile at the Area 51, so shouldn't the place be radioactive as hell (well, a radioactive hell, that is) when he arrives there later?

Probably an airburster, they tend not to create a great deal of fallout.
In numerous parts of the game, you can expose JC to intense enough radiation where it can kill him in seconds, but he soldiers on unaffected so long as you pull him away while he's still got some health left and get him first aid, an even simpler proposition if you have the radiation resistance and regeneration augs. Given that, I think an hour or less at even a really messy nuke crater would be peanuts to him.
IIRC, the entrance to A51 took place around Hangar 18 and a the nuke hit on the other side of a hill, absorbing the worst of the blast. Maybe it kept the radiation level down too.

The "Secret MJ12 facility"... how come no-one at UNATCO noticed all those bots, MI Bs, technicians and abducted scientists trailing through the base? Not to mention the Karkians and Greasels...

Probably because all said stuff only occurs in the restricted area of UNATCO base that no "clean" staff has access to.
- Granted, but they still all need to get in and out ... through Jaime's medical centre apparently. You'd think he'd notice.
  - The way you leave the MJ12 zone through the med lab doesn't mean there were no other entrances. Although I do agree that to make a medical lab, which by default requires peace, quiet and sterility, a pass-through room is a rather strange decision.
    - I think we have to go with the 'other entrances' idea ... although I'm not sure where they would be. Anyone feel a variation of the cheese shop sketch coming on?
    - You can explore the whole lower base and find no other entrance.
    - The Law of Conservation of Detail.

Liberty Island may be a wonderfully symbolic place to build UNATCO HQ, it's hardly practical. The administration and a guard I can understand, but I begin to wonder when you get to the MJ12 facility. Is there really that much trouble on Liberty Island to justify an entire platoon of patrol bots?
- Let's see...scores of terrorists, blew the Liberty Statue's head off, stole priceless Ambrosia vaccine, attacking UNATCO men...yes, all in all, there is a damn lot of troubles on the island. And if you refer to the assault bots inside MJ12 territory I'm pretty sure they were delivered disassembled via a separate entrance.
  - Not a lot of use down there though, are they?
    - They guard the armory. Figures.
    - That's great if you like overkill (given that it's at the far end of a heavily defended hidden military base and doesn't contain anything world shattering enough to warrant two top grade warbots) - what about the other ten or so medium weight bots that just sit there in the maintenance facility?
      - The armory contains a prototype plasma cannon, which there are precious few of out there.
      - There might be little world shattering stuff in the armory just then. And as for the rest, they might be there just in case of a full-scale assault on the base.
        I believe it's stated that the medium bots were taken offline due to a programming glitch. A more paranoid person than me might believe Daedalus had a hand in that...
    - I was assuming the bots were the weapons in the armoury - that's where they make repairs, reload the guns, and store them when they aren't patrolling, so...
They probably change out of the MJ12 uniforms before leaving that level. The greasels/karkians are brought in caged, and kidnapped scientists/illegal prisoners sedated for transport.

Whilst we're thinking of UNATCO, what exactly does Shannon do when she's not up to no good? I assume she's a PA/Administrator like Janice, but she seems not to have an office or workstation...

Actually, where do most of them work? Manderley has a good sized office. The Dentons presumably have to share (although Paul apparently doesn't have a log-in in game). Corporal Collins of all people has his own office, but Hermann and Navarre have a terminal set up in the corridor. Reyes surgery apparently only has two tables, while Jacobson has enough floor space to host a convention. Where are the offices?
The base on Liberty Island was founded just recently - they haven't yet accomodated.

And the Dibbuk ... oh my ... those high efficiency ethanol fuel cells must be really something if they can fly from NY to Hong Kong without refuelling. Of course they may be powered by the beers that Jock cadges off people in bars.

Also, we must assume that the Dibbuk has autopilot, toilets and a coffee machine given how long it seems to stay in the air.
Eh, its autopilot got snared by the Hong Kong MJ12 heliport without anybody even noticing, perhaps the Dibbuk's ID is still valid at UNATCO's global helipad/in-flight refueling network.
- It seems like an EXTREMELY shitty plan to use as your escape vehicle a helicopter that the evil conspiracy can randomly take control of by remote at any time. What if they hadn't flown you to a base for you to escape? What if they had crashed you into the middle of the Pacific Ocean?
  - Also, why is it that when they force said helicopter to land in the MJ12 base, there is no "welcoming committee" of any kind? The point was to force you to land there and capture you, right? so why the hell weren't there any enemies waiting? Instead they just chill in the barracks and wait for you to slit their throats. There's even multiple military bots set up to charge into the helicopter bay, but they don't send them out until after you have freed the helicopter and it escapes.
  - This actually might be justified. The soldiers are currently in the lower floors, and the helipad apparently accepts all sorts of clandestine transport all the time, and Jock was a regular flyer for them (and MJ12 hasn't entirely twigged to the fact he's a traitor by this point), so him landing is nothing special, though its more or less stated that if they discover you are with him, his life is gonna suck, hence the urgency with which you have to get his chopper disengaged from the remote lock before he and you get your asses shot off. Also, note that later he is explicitly identified to be working with you as a fellow terrorist, so they wised up after you liberated his chopper. To be fair, it does seem odd that the two guard on the roof weren't doing shit, but from looks of the wine bottles lying around, they were probably drunk off their ass, and the other MJ12 guys (assuming you sneak up on them) were also taking a break, which makes things somewhat more plausible.

What about the Ocean Lab? Why the hell did someone put one of only two U Cs on the planet at the bottom of the Pacific Ocean? Why is the crew module as far as possible from the dock - that's a hell of a long way to schlep your luggage, even if it wasn't through labs? How did people get to and from the crew module before they dug that extra tunnel? Why does the tunnel contain the world's shortest (and least safe) railway? And how the hell did they get that mover/grader down there? Surely they didn't schlep that through the greasel lab?
- Can't really explain the layout, but the location makes sense. The base isn't in the middle of the ocean at all, it's on the coast in what used to be Pasadena after South California collapsed into the sea. I imagine that this means the remains of the US leave the area well alone, considering it's probably the watery grave of millions.
- The crew module is far from the surface to keep the crew far away from prying eyes. The staff are basically prisoners, and by putting the crew module underwater the staff can be conveniently "disappeared" in an emergency. The whole base has a creepy feeling to it.

MJ12. They're apparently operating lawfully in France, yet J.C. know nothing about them, and can gun them down to the last man upon discovering a giant paramilitary base hidden in the New York sewers without the slightest comment to or from Manderley and Paul.

France is under paramilitary rule by an organization that controls most communications. It's not unlikely they just pass themselves off as a private security force and eliminate most references to themselves.
"Sir? I just wiped out a large paramilitary base underneath New York. How did I discover it? Well, an illegal arms dealer asked me to do a favor for him..."
How do the MJ12 operate openly in France yet still be called a secret organization? They've been at it for a while, as implied by the barman complaining about the "Gestapo", and a few people at least know the name. How after all this does the Internet Oracle, which data mines all communications, only speculate MJ12 to be trying to take over the world (with less than 30% accuracy at that!).
- While the organization may operate openly in France, the size and true goals of the organization are probably not known to the general populace, or indeed anyone outside the organization. A name can be easily overheard. MJ12 has it's own AI, Icarus, which can be presumed to have similar or better specs than Daedalus, and could probably run interference for MJ12 communications. Even if there was evidence that MJ12 was stockpiling huge amounts of military hardware, and was running a number of their own secret weapons projects, how could anyone tell for certain that those weapons were going to be used for world domination as opposed to, say, merely overthrowing the French government. Most people may even believe that MJ12 IS a branch of the French government. And finally, even if Daedalus or Everett compiled that information and gave it to someone, who would believe them, who would respond and which group, not already in MJ12's pocket, would have the political clout and firepower to take on MJ12?
- The restaurant owner in Paris thinks that MJ12 is an arm of the EU - which implies that French people in general do know vaguely about MJ12 and assume that it's technically above board.

How can JC die from being tranquilized while an enemy human just goes unconscious?

Who says he dies? Defeat is defeat.
- It's probably just a simplification. I mean, if I were to tranq someone who had just killed a number of my friends, I would probably get something sharp and/or heavy and finish the job. Alternatively, I'd haul the person off to my boss, who'd have him "interrogated" for a few weeks and then killed. Ion Storm probably didn't have the time or inclination include a "slugged-in-the-head-with-a-crate"-cinematic or a "sitting-in-a-chair-with-electrodes-on-your-nipples"-cinematic", and the end result is the same anyway.
- It's one thing if this happens when you're in the middle of an enemy base, but if you're among allies who could defeat the enemies and revive you, there is some chance that you could realistically survive.
- If you're unconscious for about 12 hours that's probably long enough to stop you saving the world.

The Dark Ages ending. I'm sorry, does anyone buy the idea that completely knocking out global communications would usher in a new age of world freedom, as Tracer Tong tries to argue? Most of human history has been spent without global communications, and most of human history has been spent living under tyrannical rule of some sort. His suggestion comes across as almost the argument of a mad man, or at least an alarmingly ignorant one.

In the Deus Ex universe, the world has been ruled by the Illuminati for thousands of years, who were responsible for all those periods of tyranny. Now that the Illuminati have been overthrown by MJ12, who are dependent on technology and global communication, Tong thinks the human race has the chance to be free; it will be the first time in known history that the human race is not controlled by a global conspiracy. But the sequel shows that the writers agree with you, and Tong was wrong - the Collapse just brings chaos and war, not freedom, and Tong deeply regrets his actions in Invisible War.
Despite being a rather crazy plan, I thought Tong at least made a case for global collapse. "Government on a scale comprehensible to its citizens" is a notion that stuck with me. Perhaps it indicates a difference between the real world and the world of Deus Ex. In our world, communication is bad for tyranny. In Deus Ex, technology gives tyrants a chance to control the world.
Tracer Tong's plan makes sense, he wants to damage MJ12 as much as possible since they're the ones doing damage now and after that problem is solved, they can start working on world peace. It's not a perfect solution, but then again, all the endings in Deus Ex involve some sort of well-intentioned extremism.
- Tracer Tong's plan makes a worrying amount of sense once you consider who his patrons are and what their role might be in a city-scale government (and that Hong Kong is explicitly mentioned as left alone by the PRC, so it's already a semi-model for what he has in mind).

The fake mechanic in Everett's house and the helicopter bomb just raises a huge number of questions. Firstly if MJ12 can get a spy into the building why not just blow up the entire place, attack the residents, SOMETHING. More importantly why the hell to they wait to activate the bomb in the copter until JC gets to Area 51, once JC doesn't need it any more? Ever consider how much shorter the game would be if they just blew you up over the ocean?

While Page does get some use out of JC by having him get the UC plans from the Ocean Lab, I'm not convinced that none of their agents could manage it, and without the inconvenience of giving the plans to X51. Even then there is no reason to keep him alive once this has been done.

On the subject of Everett, if he's so paranoid about hiding where he lives, why does he let you and Jock use his personal helipad at all? Wouldn't he just have his assistant drug you again and take you to some randomly selected area big enough for the chopper to land?

Everett is only concerned about who enters his home and not who leaves it. (His paranoia is justified though, given the mechanic who brings a bomb in with him.) Although why he would still trust JC after he kills Lucius is a bit of a mystery.

If Page can see everything through JC's infolink why doesn't he use the information to get the drop on JC and the allies he contacts? Just imagine if you were betraying every ally you even talk to by betraying their presence to the enemy.

If I remember correctly the Aquinas Protocols and Icarus weren't activated until about the same time JC reaches Paris. JC's only there a short time before meeting Everett, who proceeds to run interference (somehow) and it's not until he reaches Vandenberg that Page has complete control. By that time it's a bit of a moot point though, as everybody tends to know what everybody else is doing by that stage.

You're sneaking around in a top secret military base. One of the guards almost spots you but you manage to get behind cover just in time. The guard responds with "Must have been a homeless guy" and walks away like nothing happened. Spot anything wrong here?

It's even worse if you get them to say 'I though I saw something! A man in a coat!'... 'I must be hearing things'.
- It wouldn't be the first time a homeless guy had snuck in. "I'm the captain here!"

One of the MJ12 troopers randomly says he will make commando in a 2 months, suggesting it is a basis of time to become a commando, but at the end of the game, Bob Page sends the troops that killed JC's parents to fight him but none of them are commandos IIRC.

Page sends the guy (note: singular) who killed JC's adoptive parents and he's an MIB. The grunts take a different promotion path to fully-integrated MJ12 members.
Was I the only one thinking that whole little exchange was a load of crap? Like, i thought Page was just trying to get JC angry. He was a clone, right? Why would he have parents?
- It was mentioned some time earlier that he had foster parents, who despite being employed to be parents still had some affection for him. The game gets a little confused by the end though, when some sources state that he underwent growth acceleration and memory implants while others say that he went to school and had adoptive parents. It's all a bit up in the air at that point.

Am I the only person who, after shutting all the doors to the Karkians and Greasels, Greys, and bots, then deciding which ending path to pursue, feel disappointed that I didn't get a final, climatic battle with Bob Page? I conserved a bunch of ammo and got myself to full health and power because I had myself psyched up all game for the final Big Bad fight, then the game ends by flipping a switch...

On the one hand, I hear ya. It's always nice to have a huge punch-out at the end. But, on the other hand, I felt that the cerebral nature of the Page "boss fight" made perfect sense -- logically, thematically, and trope...ically. Think of it this way: you're a nano-teched warmachine; a born-and-bred killer. Bob Page is a schemer and a scientist, but he's not the muscle. He always had other enforcers (Anna, Gunther, Simons...) to do the dirty work for him. It's that old Big Bad vs. The Dragon concept. You beat down the brawn, but you outwit the brains. And ending the game on an essentially philosophical question -- not by pulling a trigger, but by "flipping a switch" -- really felt right to me. It felt like the perfect way to wrap up a game that'd have you pasting gangster against the wall one second and having sociopolitical debates with Chinese bartenders the next.
Oh, I remember how psyched before the ending and final fight with Page I was... I asked my friend, who already finished DX, for some advice on how to defeat him. Friend answered with a poker face: "You know what? Let me know if you have any troubles defeating him, and I'll help you then."

This is obvious, and doesn't even need mentioning, but... The intro. Totally awesome. Totally doesn't make any sense at all. Everything Page says! He complains about the Illuminati, which has essentially been destroyed, and the remnants of which are under his direct control. He complains about Savage, who is actually such an insignificant worm that Page doesn't even try to kill him until JC tries to contact them. Then, most nonsensically of all, Simons says, "We have other problems..." and Page goes, "UNATCO?" What? UNATCO is just a pawn... under Page's control! I know, I know, the intro can't say that... but there must have been a way to write a script for Page that lets him rant and rave and chew the scenery without saying things that we absolutely know aren't true.

The conversation seems to be happening at a time when they are securing their position, and these things haven't been fully put under control yet.
Yes, I didn't understand how much time had passed. It may be a decade. How long do Dentons hang around?
- Simons specifically says that JC will be ready for activation "within six months", so it's half a year before the game starts.
Actually, it was Simons expresssing concern and Page being dismissive.

Page: (on the Illuminati) A bunch of pretentious old men playing at running the world. But the world left them behind long ago. WE are the future.
Page: (on X-51) Our biochem corpus is far in advance of theirs, as is our electronic sentience. And their... ethical inflexibility has allowed us to make progress in areas they have refused to consider.

Go in the ladies' restroom, and Manderley shall scold you, and everyone will assume you to be some kind of weirdo. But terrorizing civilians and killing homeless children doesn't have consequences and is okay. Ahh, Deus Ex.

Sadly, that's just the case with many secret agencies in real life.
It may be that word of the latter never got back, whereas someone can and will file a complaint if something happens in the office.

Why did MJ12 framed JC Denton for crimes he didn't commit? In Paris you can read warrant claiming you led NSF raid on Liberty Island. Now imagine for a second that random UNATCO grunt has friend in Paris. And his friend, law abiding citizen writes him a mail: "Dude, you must've had tough night. Those bastards almost took over your island. I hope their leader, Denton, will pay for it". "But wait, - said grunt will think - Denton wasn't their leader. He was our agent who betrayed us later. Someone's bullshitting me here". Next day rumors will spread and people's trust in Simons will drop. "Our new generation of augmented agents, JC Denton, betrayed us. He's trained, armed and dangerous. He killed many our agents and raided our armory (Mr. Carter insists he was very intimidating)" Sounds pretty scary, and it's also true story. Why not use it?

MJ12 controls the information flows. All the rumors would be swiftly rooted out, along with the people who spread them. Maybe even that e-mail wouldn't reach the recipient.
JC was only a rookie at UNATCO, nobody knows who he is. They spread the rumors as fear-mongering for the public, basically.
- After the first mission at Liberty Island, you can read an email about the incoming nano-augmentation program and a reassurance to the mechanically-augmented agents. That and a few other dialogues gave me the impression more people inside UNATCO knew about JC's abilities than he did!
It's more likely that MJ12 wanted ordinary people on the street to identify JC. He wouldn't be able to hide anywhere for very long with a few thousand people keeping an eye out for a suspicious man in a dark trenchcoat. But if that was the case, why not include some photos?
- The plan might have worked given that Gunther tracks JC down in Paris after JC is seen in the club, on the streets etc.

IRL, random tropers delete all references to the executive orders that would permit The Government to do EVERYTHING they do in the game - right up to summary executions. All they say is "The conspiracy theorists are kooks. The orders don't mean those things. I don't have to explain what they do mean, just that they don't mean what you think they mean. Move along, citizens."

The vast majority of the executive orders listed on that page have been revoked by later executive orders, so no, FEMA doesn't have that much power anymore, even if they were interpreted in a broad manner. Check for yourself.
But it was getting out of hand and it was making the entry look like an extension of of forbiddentruth.

The NSF don't know about UNATCO's plans to give JC a test, so they can't know UNATCO isn't going to be using their helicopters to strafe all the troops they have out in the open. They also have ONE sniper and they put him at ground level behind a bunch of walls. Wouldn't it be better for him to have been at the very top of the building, popping this lone trenchcoated guy who's killing your buddies on the ground? Methinks the NSF commander took his "You can't fight ideas with bullets." mantra a little too literally.

The NSF are occupying the statue to waste UNATCO's time. The leader even says so at the top ("You're too late..." and then the peaceful surrender.) Their only purpose was to hold UNATCO up while the ambrosia was moved. Bombing the statue is not an option as long as Gunther is down there.
- UNATCO probably know what the NSF are up to, so they send in JC, knowing that it won't be too dangerous.
  - You misunderstand. UNATCO may know that and is holding back to give JC a test but the NSF should have expected a much more forceful response when they invaded Liberty Island. While their aim was to stall UNATCO, if the troops had not been given the order to fall back (and especially if they had air support) the NSF wouldn't have lasted 5 minutes. And Gunther wouldn't have been captured if the rest of his team hadn't fallen back as ordered. If they had continued the assault and the UNATCO troops were covering Gunther he could have taken the NSF out. Now I suppose all the NSF needed was 5 a minute diversion and the extra time of JC's approach was just a bonus, but even then the NSF has speedboats and UNATCO has helicopters.

How much time passes from the start to end of the game? While JC Denton gets to Hong Kong unrealistically quickly, the game never seems to change out of night, and it seems improbable that everything from the raid on the Statue to the attempted escape with Paul happened in a night.

As the game progresses, JC keeps switching timezone. I've never sat down and worked out the timeline, but it's reasonable that he just gets unlucky and always has to work at night because of the timezone changes. Given that, it could have happened over several "nights".

Technically, a nano-augmented agent is more dangerous than a mech-augmented one. So why can mech-augs be killed instantly with a single phrase, but for nano-augs, they instead implemented a killswitch feature, which takes a day or so to work? It just seems like a step backwards. As the game shows, there's a lot a person can do until their killswitch takes full effect, up to and including finding a way to defeat the killswitch altogether. Wouldn't it make more sense to use the killphrase system instead, so they can be put down instantly if they decide to go rogue? If the argument was that the killswitch works from everywhere but the killphrase must be used up close, well, you could just use the agent's infolink for that, no? Simons could've transmitted the killphrase right when he realized that JC had betrayed them after sending that signal to the NSF. Or he could have spoken it during one of their conversations over these holo-communicators. And that would've been it. Game Over.

The killphrases and killswitches are the triggers, not the mechanisms. They could very well have hooked up a radio receiver to Navarre and blown her up that way. You must also remember that the ability to kill somebody by remote control is top-secret (or Domination-5F if I remember correctly). The mechanism for the mech-augs is a bomb hidden within their augmentations, something that would be rather conspicuous if found in the nano-augs. The nano-augs self-replicating nanomachines are crude, yet subtle enough that Paul didn't even suspect it possible.
- Minor correction; JC is the one who didn't suspect it possible and expresses disbelief. Paul apparently knew about it, since his response is to explain that it works by setting the nanites for uncontrolled, cancer-like (presumably much faster though still not as fast as the mech-augs' bombs) growth.
  - I meant he didn't suspect it when he revealed his defection. I doubt he would've publicly switched sides on the opposite side of the world from the only man who could help if he had known.
- Perhaps they thought that since the Dentons were clones that were given at least some false memories they thought it would be impossible for them to switch sides. They thought they had programmed them well enough to be loyal to their original cause. The infinite replication of the nanites was probably a bug not a feature, and that's why it's not as effective as a mech's killswitch.
  - The idea behind a killswitch is that it kills when it's switched on. MJ12 and JC's handlers didn't know about Tracer Tong's ability to affect the nanites, and twelve hours isn't enough time to do anything significant, given travel times. Paul and JC's killswitches are, to the people that activate them, irredeemable weapons of murder. In addition, Simons isn't patient enough to wait for the killswitch, telling the troops to kill JC and Paul instead. The killswitch is a fail-safe, and a good one. It's only by using resources that MJ12 didn't know about that JC (and potentially Paul) are able to survive it.

How is it that Paul is too weak to climb out of a window and up a ladder, but is more than capable of winning a firefight with a dozen soldiers in a hotel lobby?

Why do they take JC prisoner after he defects? Page turns on his kill switch and orders the troops to gun him down, and then they put him in a cell for...what, exactly?

Same reason they keep Paul alive; they want to study the way you die.

Why did they bother with the plasma pistol holdout? It'd at least make sense if it could one-shot, but it doesn't do that even to common mooks... yet it has a handheld model and full weapon functionality.

And they're fairly common, to. That it's a held weapon, maybe ION intended more for it. DX's Wikia entry said it came from a design to replace the stealth pistol (neon black blobs instead of green? heh) But it's just functional piece of decoration. It's not even that great for self defense or diversion