Just by the name Pathfinder and the fact that everyone has been crying for exploration yeah, it does seem obvious that it will be the new "Inquisition" so to speak. Your job will be to scout out new worlds for Earth or whatever. The "A R K C O N" makes it seem like humans are fleeing Earth, so it could take place prior to or concurrent with ME3 as some kind of Reaper avoidance thing. Or the aftermath of ME3 has left a wrecked planet, shattered relay network, and numerous alien armies stranded on Earth. So they're looking for a new home away from Earth.
Ha just kidding, that would rely too heavily on continuity, so it will probably be a totally unrelated calamity that befalls Earth
You know what I would like, that wouldn't involve a galactic calamity threat? If you simply play a team of explorers who go to another galaxy, something goes wrong and you can't get home.
The point of the game is gathering up what you need in order to get back. No giant threats, simply having to explore and deal with the races in the new areas in order to get what you need.
I don't think that would happen, because you'd have to have minimal contact with the current races, but it would allow for a very Star Trek feel to the game.