User blog comment:Kogath/Monster Hunter 4 Ultimate for the Nintendo 3DS/@comment-6050823-20140126121519/@comment-6050823-20140126150716

For right now, I'm guessing since those four hunters were researching Goa Magara and then founding out what it turned into in the Siki Country before the chief sends you to kill Shagaru Magara, that they are now researching the new Desert and a few of its inhabitants, including one particular monster(Assuming that the new Flagship Monster is in the Desert), and that the Guild is finally looking at wherever the 4th Generation is.

That's just my theory on its possible story, if it has some story like MH4.