I think it was a large NORAD like bunker facility way larger than all the other bunkers in the game. As it was just too hard a nut to crack, the only option left was to completely level it with mini nukes.
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First, we don’t know how vast this network really is. I’ve been even joking that at first there was bunkers and Ostertorn been build above them.
Second is how deep FOA been digging? Hints are Muskudden Port complex and North Coast FOA Facility.
Third, about cause of destruction my guesses:
- It wasn’t nuke for sure. At least not external - for crater like that blast would be powerful enough to flatten out the whole Farmlands and beyond; for scorching marks like we seen the blast wouldn’t be sufficient to dig it this big. Internally - more likely, but it would be rapid explosions of all these “dirty” rockets for Apoc Harvesters and Reaper.
- Reaper directly involved - there’s a reason why thermobarric explosions are exceptionally deadly within bunkers/buildings. Considering that SuperTank’s “butt-hurt attack” we observe in the open area, that chemical it releases and ignites has waaay bigger volume of explosion than this pre-fart cloud.
I assume that there’s no direct pathway big enough to safely transport the Reaper from FOA4 and been disassembled there, transported, assembled.
1.1) there were no way that Reaped could exit complex on one piece. So it dug itself out.
1.2) there was some crucial clue/piece/weapon/alien etc that FNIX deemed too dangerous to keep/guard and it was better off to get rid of it, Reaper blew it up nice and clean, whlie getting to area where it would be more useful (Himfjall already infested with nasty Apocs and Reaper won’t add much).
1.3) there was incident around time of activating Reaper, likely during testing systems. And it’s butt-hurt was too strong for complex to contain it from inside, but shield system was robust enough for machine to survive. - Reaper indirectly involved - may be that tunnel network was strong enough to withstand any punishment from a single Reaper. But what if there was two Reapers blowing stuff up? Dozen?
I talk about equivalent of chemicals and munitions exploded simultaneously, measured in “reapers”.
2.1) Judging by blast radius (scorched earth around crater), puddles of green slag, lots of ammo boxes, terminal with it’s chematics etc, I guess it’s the real birthplace of The Machine (since it’s hinted that Reaper is FNIX’s project). FOA4 was used for it’s specialized assembly line that can handle hazardous and strong materials to materialize SuperTank in metal. The space that is now crater was either vault for storing munitions for Reaper or actual munitions factory, that was able to tend to Apoc needs.
2.1.1)FNIX couldn’t handle proper maintenance and caused hazardous chemicals leak (machines didn’t bother with gases in bunkers and even weaponized it) which was set off by something small (there’s incediary ammo for ApocTank/Reaper and flamers). Over time leak was filled that space with that very potent aerosole explosive and set off. That would explain crater shape - even small “secretive” munition factory/storage still would need extensive digging and concrete isn’t that strong, considering crater appear in rather soft “farming soil” withoud much of bedrock like other known underground facilities. With spacious area like that one at FOA4 and it being filled with that “special fart chem” the workshop was rather weak and sheer explosive pressure would literally blow upwards it’s roof and grind it’s relatively thin bunker walls into smooth slopes, yet somehow preserving some concrete around. It wasn’t that deep in the first place, and excess aerosole spreaded and scorched with about same ratio as Reaper’s thermobarric attack (gas cloud to fireball ratio). That would also explain uneven destruction around crater.
2.1.2)Some accident happened during Reaper’s arming up that ended up in rapid fill up with thermobarric cloud and it blew up. May be mishandling equpment, may be FNIX been grinding gears of production line without/unable to do proper maintenance (we still don’t know where and how machines and structures were built). Reaper was activated and either was or wasn’t there, either moving nearby or just in stand-by - it had enough time to react and escape explosion or shielded itself and dug up itself/helped out in the worst case.
2.1.3)There was test runs, that involved Reaper’s armament and some accident set off explosion/munitions stored, due to weaponry being too powerful for tests like these/facility wasn’t intented for this purpose and didn’t have enough structural strength to protect explosives/ammo from Reaper. - Reaper itself has nothing to do with this and “craters space” was either sabotaged prior by still present humans just before the demise/abduction* or there was a skirmish that led to severe damage of facility and FNIX didn’t fix it in time for some reason, which needed some external “kick” to set it off like fighting nearby or by the tremble of sheer combined mass of machines.
* command bunkers are for some strange reason were devoid of bodies and has little to none signs of fight, just some of them have scenes or “forceful entrance”, but nothing more
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My idea is similar to the quoted one:
But with some differences.
I think that the Skinnarbol was the main development bunker for Reaper, evidenced by the nearby terminal with it’s blueprint. And during the development or assembly of Reaper’s armament, something went wrong and the whole assembly area went sky high.
It is impossible to tell what exactly triggered the explosion but it could’ve very well been that one of the assembly ticks had malfunction and pointed it’s laser to wrong spot, thus triggering the explosion.
The following shockwave was enough to blow out from the bunker complex, forming the Skinnarbol Crater in the process. Though, the bunker complex was sturdy enough and/or explosion wasn’t powerful enough for the shockwave to travel much further from Skinnarbol.
This explains why the devastation is contained in the small area. However, shockwave alone isn’t enough to set trees on fire. For that, i have another idea.
After the initial explosion, the highly flammable gas, that machines use, leaked into the crater, filling it. And it found the ignition source, thus creating 2nd explosion and sending wall of fire all around the Skinnarbol Crater area, burning houses and trees.
I also think that after that “setback”, FNIX learned from it’s mistakes and assembled the Reaper at some place else (best candidate being FOA2). And FNIX continues to make Reapers in another facility. Latter explains why new Reapers are able to spawn, once player takes out the active one.
As of why only one active Reaper can be on the map at any given time and not several, my guess is that FNIX doesn’t have enough computing power to control more than one Reaper at a time.
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Well, your theory about “double explosion” started up me another though train that has no brakes. 
A bit off-topic, but I still drop it here.
What if “thermobarric explosion” that used by Reaper isn’t cause, but consequence of “crater incident”?
Like FNIX been gathering pieces of the aftermath and concluded at “I want that to be a weapon!”
We don’t know for sure if there canonically a single Reaper or FNIX somehow got enough advanced resources and facilities to to regularly rebuild it. Unless I see two side-by-side my headcannon will register it as single unique entity.
Back to topic: most things I’ve covered by other words, but may be not that eloquent.
The part about “double explosions and fireball outside”: points about “weak concreete”, “soft farmlands soil”, shallow building are about deliberate design choices for that munition/chemical factory/storage.
Thing is that any cause that will lead to explosion will need countermasures. Concentrated explosion against bedrock especially underground, like other bunkers/FOA facilities, would inevitably cause shockwave that would be equal to earthquake, so hipothetical “ammo storage boom” certainly will set off and destroy the rest of workshop. “Weak concrete roof” and shallow dig for factory will cause least resistance upwards, “soft soil” damp a bit shockwave. The placement under one of “plainest” areas around (or rather with very wide “bowl” shape) with least possible settlements to be not suspicious will secure least collateral damage. “Weak roof” point is about that within single blast all the fuel didn’t burned and a lot of it was spreaded around. Think of boiling pot - overpressured steam will cause the lid to jump. Same here - “roof” itself was sturdy enough to preserve it’s “shape” for the most parts, but collumns and other support wasn’t, so this “lid” for a moment long enough under very high pressure horizontally spreaded most of fuel along wide open area due to “shockwave”.
About the “double explosion” - I’ve had an itch that I’m still missing something.
It still could work out:
- puddles with ticking noices (that is what does that ticking noices?) hinting that there were “dirty” bombs/rockets. These are highly unstable munitions and caused initial destruction. Shockwave from it caused damage for what appears to be tanks with highly volative “fart” that started to fill up all the holes. Some flashbulb shorted and ignited it, causing even more destructions and paint a new wasteland over farmlands.
- there was “few” consecutive thermobarric blasts. “Inner” was powerful enough to crack through roof and a cistern of it under big pressure set fly upwards and break somewhere outside or at least burried very shallow. Some debris damaged it, gas rapidly spreaded in and out of crater and then something still burning/sparking ignited “outer” blast that made “wasteland” area.
Other cause would be (mis)handling unstable chemicals.
- However advanced were FNIX and computing power in it’s possession, it still wasn’t enough to perform scientific calculations and control machines. So it resorted to method of “poking with sticks” (sci. for “empyrric research method”). And then extreeme exothermic reaction dug us a grey sandpit.
- Or probably during “FNIX Rising” events teenagers destroyed/hacked “just right” servers that supervised these researches and sudden server failure led to momentary mishandling of chemicals, long enough for turd reach fan.
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They mention this in some of the audio tapes or someone talked about it. I believe the machines were collecting bodies to experiment on them but later stopped. I guess they learned enough about us. As the bunkers were strategic points they would have been hit early on by the machines and therefor those bodies would have been some of the first taken.
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The crater was created by the reaper tank. It popped up when the reaper was added and the reaper blueprint can be found there. It was in the underground bunker we see ruins of and was able to blow itself out.
Yes, but it’s unclear what exactly happened. I mean what kind of explosion. How was it triggered, etc. There is no info on this, only visual evidence And the fact the Reaper was introduced, which sparked a lot of ideas, and conjecture.
Well, the reaper does have an attack that causes a massive explosion, so probably that.
Yes probably the thermobaric blast in combination with explosives/fuel in the underground bunker. Still there are also nuclear theories. Also the why is untold, was it deliberate or accidental?
So it’s not a story fact yet.
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Well, we know the reaper is one of FNIXs own creations, as seen in the blueprints description. He took over a prototype of a new tank shortly before the invasion and made it his own. With that in mind, I’m guessing it’s deliberate.
Discussion moved to proper topic.
//Mod
Maybe bunker 66(6) is a maintinance entrance for the tunnels at the crater? so what if bunker 666 is a way in
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Does anyone know what happened to cause all the destruction in the farmlands?
If you do let me know I can’t figure it out
I believe it is the events from cataclysm day.
Same discussion topics merged.
@Iris read the above replies to find out most plausible theories.
//Mod
Ok I know I asked what it is but I think I have a theory the Reaper didn’t do it at all but it was manufactured there or had some relationship with the place. I understand you’ll all say “It was the Reaper what are you talking about” just hear this. The crater was just a test by FNIX for something far worse something like all the tank classes merged into one really big really deadly and really hard to get to spawn. If you did make it spawn you would most likely need something like ever type of tank in one region all max level, including the Reaper and the ln you’ll face FNIX’s prized champion (it would most likely appear away from you) and I have a feeling if any of this is true then Avalanche could intend that this is a kind of final boss that might be spawned and downright controlled by FNIX and is spawned someway else than rival relation. If you liked this theory just hit the little heart 
This isn’t a theory it is a correction you see I meant not all of the types of tanks yet I meant all of the classes there are combined as if FNIX tore apart each and reassembled them into one big demonic horrifying tank.
Sorry for this I just needed to make sure you all knew what I meant or I needed to make sure those who didn’t understand, understand
BYE BYE
Your idea is similar to mine, which i posted above:
There is clear evidence in the lore of Reaper's existence. (Spoiler alert!) Click here to read.
The main assembly was already constructed: body and appearance.
Reaper before FNIX finished it, as it appeared in FOA4:
What FNIX did, was adding weaponry (from other machines), shield generators and thermoboaric explosion, thus completing the Reaper. FNIX even kept the original code name: “Grim Reaper”.
Reaper stats:
Base body
- military tank
Weapons
- shockwave stop (all tanks come with it as built-in)
- stinger/FNIX tick deployment (in use for apocalypse and FNIX class machines)
- incendiary machine gun (from apocalypse tank)
- radiated missiles (from apocalypse harvester)
- biochemical gas (from apocalypse harvester)
- anti-weapons shield
- thermoboaric explosion
With that, only Reaper weaponry is a mash-up from different machines. While the rest (and most) of it is normal.
While it’s unknown, but it is very likely that FNIX developed the thermoboaric explosion feature for Reaper and that thermoboaric explosion was the reason why Skinnarbol Crater was created. Triggered by the manufacturing error, as i theorized.
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Wow what a chance because I didn’t even read yours