First off, just to set things straight, F.E.A.R. Files is a compilation package of both the first F.E.A.R. expansion Extraction Point (converted by Day 1 Studios), and the new expansion Perseus Mandate for the Xbox 360, which is being developed by Timegate Studios for both the Xbox 360 and PC. PS3 owners are out of luck, for the F.E.A.R. Files is an Xbox 360 exclusive. Both packages will be standalone and will not require the user to have any previous versions of the game.
With Perseus Mandate being the second expansion, it does not follow after Extraction Point, however Perseus Mandate sees a story that happens in the same time frame. A second team of F.E.A.R. operatives has been dispatched to the Auburn district to find out what happened to the original F.E.A.R. squad that was sent there.