The reason that Joseph Seed was so certain that The Collapse was coming is because he schemed to bring down the Apocalypse upon the world.
Here's some of the circumstantial evidence that I found to support this theory.
When you meet Selene and have to retrieve her medical kit, it is lost inside the launch tube of a Minuteman III silo. I don't remember if they ever explicitly call it out as an ICBM silo, but that's what it is. The launch tube is empty, so whoever was crewing it managed to launch their missile.
When you go inside of the silo, there are notes that indicate it had been taken over by the Peggies sometime before and during the collapse. There's no sign of the original crew but there is a note from one of the Peggies indicating that they had all been very ill after the collapse but then Joseph Seed himself came to retrieve them from the silo. Which assuming it wasn't a hallucination caused by radiation sickness, tells us that Seed knew they were there.
Then, when you leave the control center operations room from where the missiles would be launched, there is graffiti over the exit that reads "some day you will thank us."
Then, when you play the expedition mission Government Plane Wreck, there's a note that reads: "Just updated the President: latest Intel has the empty quiver on US soil, somewhere in Montana. We are on route and will have boots on the ground in 4 hours. An associate of mine is reaching out to old contacts who have had dealings with the local militia. However, the news of the potential evacuation of DC has sent a lot of rats into hiding."
Empty quiver is US military jargon for the loss or theft of nuclear weapons. Seems likely that this is really why Willis was in Montana during the events of Far Cry 5… I mean, how likely is it really that Joseph Seed would be able to get (or even care about) Russian blackmail materials?
Joseph Seed's certainty that The Collapse would happen wasn't divinely inspired, he knew because he engineered the entire thing
Counterpoint: it shouldn't actually be possible for a silo crew to launch the missiles themselves. However, it wouldn't be the first time that the Pentagon has not been completely honest about the safety measures required to prevent a crew from deploying thermonuclear weapons without proper authorization (Mark 39 gravity bomb, I'm looking at you). FWIW, I am pretty certain that a silo crew would be unable to launch without proper authorization, but this is not real life, and it makes a very neat plot twist that puts a very different complexion on the events of both games.
So there you have it. He might look like a harmless yoga instructor with a taste for 1980s era sunglasses, but Joseph Seed is actually history's greatest monster.
TLDR: Joseph Seed sent Peggies to take over a nuclear missile silo so he could start The Collapse by attacking Russia. The government knew that a militia group in Montana were involved in the loss or theft of nuclear weapons and were sending a special forces group to take the silo back when the shit hit the fan.
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