Have you ever been at Bunker 666?
Listen…
(Relating to text from Note 7)
I haven’t read all the texts yet, but I think that there are as of yet no clues where Fnix moved the humans to.
In the “Good Night” mission this conversation took place:
Veronika: “All the data say there should be a lot of survivors here. Where did they all go?”
FNIX: “Worry not. I moved my precious resources somewhere you will never harm them.”
As for why they were abducted, wasn’t it so that it seemed that Fnix wanted or is using human resources (via brain interfacing) and to use the brainpower to remotely control all the human-made machines?
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A keen eye will spot all those people on screens during the mission “Behind the Curtain” 
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Ah, so a keen eye probably made screenshots of those screens, yes? 
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Yes, it would be logical for FNIX to physically instancing itself and thus need human brains. FNIX also claimed it can never be destroyed so I recon every human interfaced with have FNIX are not human anymore. That could mean Elsa is FNIX too.
In Good Night end mission dialogue:
FNIX: “You may kill me as many times as you wish. But I will spring forth again from my backup memories.”
…
Veronika: “There’s someone I love out there who I need to find before it’s too late. I’m sorry, I wish I could stay, but I can’t lose Elsa, too. But I’ll keep in touch. Promise. Stay safe out there.”
[Edit: Inserted dialogue texts from Good Night mission for clarification.]
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Janek describe how FNIX works by his findings of what he can observe through the machines behaviour. Machines work to produce electricity, powerlines and the construction of bases we assume of some strategic plan by FNIX.
In Note 2 he didn’t mention the powerlines at that site that goes into the water, Janek could only observe what was going on on the surface. Those powerlines may also have been a later addition in the game?
From these notes comes the question if machines are remote controlled as designed by the FOA and thus are forcing FNIX to comply with time-sharing processing in a real-time based system. This could be a vulnerability where attacking hoards of robots or the Reaper will distract FNIX’s defences reducing processing power and open up for Veronika to hack the mainframes in future missions. If FNIX instead utilize multiprocessing and multithreading with human brains then this won’t work.
There are no similar notes on Himfjallet Island. I suggest some Iron Church Notes leading to FOA2 would be needed in the game to complete the understanding of how FNIX operates and find it’s vulnerabilities.
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It is not clear to me who Veronika is talking to when she says:
It would be strange if it was FNIX, even if she thought she was talking to the Svante part. No she must have been talking to us, the players.
But she said it because she lost Svante and Calle her friends, and she doesn’t want to lose Elsa too, because she loves her romantically.
I don’t think that FNIX uses humans who are still able to interact with others. The humans the FNIX uses are connected to an interface, somewhere safe from the resistance.
Not sure I can follow your thoughts. It seem to me that when Janek wrote Note 2 to Basse, he hadn’t yet seen the powerlines or just did not mentioned them, because he was writing about the machines’ caches (red vaults), and the resources they could get from. In his third note however, he did mention them.
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Some questions someone might answer…
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Note 5: While out stalking the machines to gather more information, Janek discovered some horrible furnace they built, larger than the Devil and twice as ugly. Where would that be?
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Note 7: In any case, they spotted Janek when he got too close to their fort, and tripped an alarm. What FNIX fort is Janek talking about?
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Note 8: This town is so quiet… …I can still see the smoke in the distance of my old camp. (Måsskär?) What town do you think?
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Note 9: The maszyny have erected a gigantic… furnace? core? shrine? near the town. What did Janek mean with that Furnace?
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I played through all missions and covered most areas before installing Alpine and FNIX Rising, I haven’t noticed any of these things too. It is like furnace-things have been moved or he is exaggerating things, but to what end? I don’t think FNIX missions destroyed those things any way. Smoke however should have vanished if letter were written some time ago so that one is understandable.
@Madchaser yes that closed bunker is creepy with or without the funny glasses.
(Off topic: Have you been to the haunted barn on top of the Norrmyra Artillery base? I just got there today and also noticed that bunker below the barn have a lot of locked doors. No weird sound though, just silent. But lots of rooms to keep prisoners? -2508,-2755)
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There is a prison with some dead bodies in a cage at the fnix outpost next to Stenungsnäs.
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True, that fnix prison is a better fit to where people were taken. That Norrmyra bunker better fits an Iron Church hideout.
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A bunch of people dreaming they are machines 
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Added Janek’s timeline of his journey.
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I had some private discussion about who Veronika is talking to in that instance, and the consensus was that she was talking to us, the player.
In “We are the Resistance” mission
Elsa Khorsandi left half of her military identity badge in the cellar, in the hope that Veronika would come back and find it. That was her way to say: "I’m outta here, but I’m not dead."
On a piece of paper found next to it, she wrote: “Veronika, remember, we are the Resistance!”
It also seems that Veronika and Elsa, who both shared the same shelter at Ängsnäs Manor, had developed some romantic relation. That would be a reason why Veronika did not want to lose her.
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don’t remember much about the final mission, haven’t played final mission in a few years, 
don’t remember, but do the people move in the camera
Can’t say if they did or didn’t, the monitors went out one by one as soon you get a closer view.
Check the monitor scene at 2:45
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