Okay so, major spoilers here. This is the story as I’ve understood it from playing through the story two times.
The Cold War has ended, and the Swedish military have invested heavily in robotics. Their idea is to incorporate automated war machines that can be remotely controlled via a single or several controllers. There are several different models ready to be rolled out depending on the kind of emergency. The first idea was to control the machines from secure command bunkers, via computers and various other equipment but as research went on a team of scientists working on neurological interfacing were brought onboard at the FOA facility.
The team were working on a way to interface with the brain directly, hooked up to various animals, via an operative system of their own design. I can imagine that the scientific benefits for this would be quite beneficial in the long run. They had some success, and so the swedish military contracted them to incorporate their technology with the machine program. The goal was to have a human being (or several) control war machines in the field, sparing manpower and resources, through the neurological uplink.
The leader of the science team, Svante von Ulmer, disagreed to this at first. The very idea that their research would be incorporated onto a weapons platform seemed absurd. He had several meetings with the military’s officials about this, and as the project dragged on he became pressured to sign on as one of the first human subjects. At the same time he had problems of his own, he was sick with a life-threatening disease.
So, he signed. The operative system was dubbed FNIX (bit of a Phoenix thing going on here), and surgery took place to incorporate his consciousness into the uplink. And it all went downhill from there.
Perhaps it was his way of revenge against the military for what they wanted to do with the project, perhaps it was his way of living on after the disease would have killed his body. Maybe he was just tired of life as he knew it. Maybe the procedure just made him insane.
The machines came to life, and similar to Skynet from The Terminator, immediately grew out of control and began to take over. With the military having invested so heavily into the project, they were easily overwhelmed.
It started small-scale at first. Radio communications were blacked out. Key personnel vanished. The scientists that were on the FOA project were eliminated by Machines to preserve secrecy, but one got away and tried to inform the military of what was about to happen. She failed.
By the time the player characters arrive back to Östertörn by boat, I estimate it’s been just a few days after the Machines took over. We encounter prototypes in the archipelago, it’s likely that FNIX estimated that resistance here was light, so it sent forth the weakest machines to deal with it.
So the players work towards finding out what’s going on, and soon manage to come into contact with Russian forces, who agree to help shut down FNIX. You’re given an EMP bomb, and sent to the FOA facility. There you encounter Svante Von Ulmer’s consciousness, echoing into yours.
By the way that he talks, it’s obvious he no longer cares about the project, or other human beings. He has other plans, and although you walk into the FOA facility with that EMP he’s surprisingly calm. Even as you find the FNIX mainframe and set down the device, he urges you to run as he’s sure the Russian military counted on you dying when the facility was destroyed. Does he know something that you don’t?
As the EMP goes off and the facility is brought to ruins, you emerge only to discover that it’s too late. The Machines are still very much active, and although you destroyed the source, FNIX must have already found means to spread elsewhere. The Machine Apocalypse has begun.
That’s my take on the story, anyway.