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(Spoilers) Why are the villains so obsessed with Orchid?
- The Orchid is basically a poison. Not even a very efficient one, because Jensen just shrugs it off, like it's nothing. For other people - there is plenty of time to give them an antidote before they die. Why does Marchenko keep using it, event if it unnecessarily complicates things? Let's list all the examples:
- Rucker - this is the only case when it works flawlessly.
- Jensen - why not just shoot him in the head?
- Miller - again, why not just shoot him in the head? Bonus points: at this point Marchenko already knows that Jensen is alive, and it implies that Orchid is not 100% effective. For all he knows, Miller may be immune to Orchid, just like Jensen.
- Brown and other diplomats - Marchenko's men already control the entire building, why not just shoot them? Or blow them up? Instead they go to extreme lengths to smuggle the Orchid into London and covertly poison their drinks. If they have to poison them for some reason, why not use something more deadly?
- With Brown and the other diplomats, Orchid is a pretty horrid way to die, which is the point. ARC was framed for stealing it. If Brown and the others die a very public and horrible death at the hands of ARC, everyone in power that was on the fence will accept the Human Restoration Act.
- He may be using it as a prototype for the Grey Death. It would make sense to test a non-viral, easily controlled version of the bioweapon to make sure the method of action works, before moving on to contagious versions. Also, as far as Megan knows, the Orchid wasn't supposed to be a weapon at all, but a delivery system for Adam's pro-augmentation genes. It's just an unlucky coincidence that the "remove" component of the Orchid was finished before the "replace" component was.
- Jensen only shrugs it off because he has an exceedingly rare genetic mutation, one that only a small number of people know about, and most of them are in disbelief when they learn of it. Marchenko's masters know, but it wouldn't be the first thing they didn't let him in on. For Miller, he was attacked only shortly before you reach him, and he does not last long if you don't give him the antidote (barring the player deciding to take their time getting there).
- It's also a tasteless and odorless poison that's hard to detect (the coroners examining Ruckers' corpse had theories but those were scrubbed from the report). Still seems like overkill seeing as they weren't trying to make Jensen or Brown's deaths look like accidents.
(Spoilers) Marchenko and his kill switch
- Why does Marchenko have a kill switch to begin with? Hell even when you get past that, why would he misplace it?!
- This one ties into the original Deus Ex and is also answered in this game. The Illuminati were the ones who created the kill switch for him as a means of controlling him and ensuring he stuck to the plan. They did the same to two of their augmented agents in the original for the same reasons. He never misplaced it because he would have never known where it was, the Illuminati would have had a mole inside his group with orders to use it if he betrayed them.
- This question is only answered (overtly) if you manage to find the Guide Dang It! location of the killswitch within the GARM facility. A coded message written to Jorge and Yevgeny, two members of the facility (which is actually written from Bob Page, under the name "Mister Majestic"), mentions that he has given the killswitch to the employees to be used as a safeguard in case Marchenko doesn't follow their plan, as said individual doesn't overtly trust him. You can only get said killswitch by activating a hidden switch wedged between a wall and a set of lockers, which unlocks a hidden compartment at the bottom of a locker that has the killswitch. In the case of London, it is also presumed that the second killswitch (the one placed in an unscannable box near the kitchen) was brought over as such for the exact same purpose.
- Miller seemed pretty genuine about wanting to stop terrorists in general an Marchenko and ARC specifically, especially at the end of the game. Adam even says that he believed he wasn't working with the Illuminati. But we saw Miller talking to the Illuminati and taking orders from them. Who's side is he on?
- Miller was taking orders from Manderley, who is his legitimate superior in UN hierarchy. He either doesn't know Manderley's intertwined with the Illuminati or he can't do anything about it.
- When you first meet Marchenko he talks at great length about augmented rights and how ARC needs to be more forceful to secure those rights. But he's actually working for the Illuminati, who wants the Human Restoration Act to pass. That was the whole point of their attack at the end. So is Marchenko actually against augments? Even though he himself is an augmented person?
- Basically, Marchenko doesn't care for ARC nor Rucker; he believes they're only dragging out the inevitable conflict between naturals and augments by wasting time on attempts at brokering peace. He wants to force augments into a corner to the point where they have no choice but to fight, and he's planning on doing so by making ARC look responsible for both the bombings in Prague and the attack on the Santeau Group's executives in London. Notice how he killed off the ARC members he spent time recruiting and training to be terrorists before leaving the GARM facility? They're just scapegoats to him.
- Marchenko could be full of shit too. It's very possible he's working for the Illuminati fully aware that he's going to destroy Augments as a species—but can't do anything about it because they have his Kill Switch (and possibly his family). In that case, he's just a very good actor playing the role of the False Flag Operation leader.
(spoilers) Adam's hospital stay after Panchea
- If one follows the "Mystery Augs" sidequest, Adam discovers that there are huge holes in the "months in a coma" theory; specifically, all those augs that Sarif stuffed him with? Have serial numbers. Anyone who looked up any of them should have instantly known who he was, meaning him dropping off the radar is incredibly hinky. However, the System Rift DLC has Pritchard track Adam down using the GPL functions in those very same implants. Where was "Nucl3arSnake" during those months!?
- Black Light (one of the tie-in novels) explains pretty much all of this. The facility Adam woke up is run by the WHO (read: the Illuminati), and had jamming equipment that kept Adam from contacting anyone (and presumably blocked his GPL tracker, similar to what happened with the scientists at Omega Ranch). And Pritchard was the first person Adam contacted as soon as he got far enough away.
- In short, Adam is Adam and he's only missing a couple of months after being fished out of the water. Months he was kept sedated and operated on.
Illuminati meeting room
- That room at the beginning where the Illuminati meet, what's the point of it? If no one is actually showing up, why have a meeting room at all why not just communicate through view screens? Why sit in the chairs?
- It's just a fancy version of the Neural Subnet that Miller has in his office.
- It's also suggested in at least one communication (the hidden email message between Elias Chikane and (presumably) Stanton Dowd found in Chikane's workshop) that the Hong Kong office acts as a sort of router/central send point for messages to or from operatives, likely because it has greater security. As later events in the series suggest and/or outright show, several of the Illuminati members are Properly Paranoid enough that although they don't want to meet in person, there are certain purposes they require having an "avatar" for (case in point — Delara Auzenne utilizing Elizabeth Duclare's identity during the meeting and speaking to Debeers at its conclusion, or Janus/Volkard Rand wanting the inside track on conversations and visual tells.
Neural Sub-Net security
- The Illuminati, an organisation obsessed with the control of information flowing around the world and shrouding themselves in layers of secrecy and myth... gave Miller a communication system that records every single conversation had using it, even if he wasn't part of it, and even if it involved matters that he really shouldn't be allowed to know. All he'd have to do is look at his communication history, and see Manderley admit that the VL attack in San Francisco is made up.
(Spoilers) Jensen's new augs
- Even if he's the Illuminati's Manchurian Agent why put a load of experimental augs withing Jensen? He won't be a good test subject since he's unaware of their existence and they risk exposing what they did to him if he ever discovers them. Even if the goal were to make him go berserk and kill his allies that wouldn't explain non-combat, non-lethal augmentations like Remote Hacking or PEPS. Plus a simple killswitch would be more reliable and subtler.
(Spoilers) The Harvester
- If fought Daria reveals she has advanced experimental combat augmentations including TITAN and the Icarus Dash. Even if the goal of her experiment was to produce mind-controlled soldiers or manchurian agents why leave the augmentations online rather than hiding them like Jensen's? And if Versalife lost interest in the experiment why leave her alive when any coroner who found her brain chip or experimental augs could cause problems for them?
Why does no-one put together the connection between the biochip rollout and The Incident?
- We've seen with tech rollouts that many users are slow to apply updates when all it requires is clicking a button. Even with the visual glitches hurrying things along presumably a signficant proportion of augmented people would have been unwilling or unable to reach a LIMB clinic and get the new chip installed in the day or so it was available and therefore didn't lose control during the incident. Obviously Picus will be playing down the connection but anyone who did some basic investigation would immediately see that it was the non-chipped who were unaffected. Why is Samizdat merely saying the chip's release's timing is suspicious when the direct line of cause-and-effect should be obvious just from talking to one of the many non-chipped augmented people?