That is what it is about exactly Darkthunder. STOked had a chance to visit Cryptic for their 100th episode and they got a sneak peak of the next series, a cut-scene from it of the player talking to the prophets (In the form of people you've met before, just like in DS9) that basically outlines the plot.
The Prophets couldn't remove the fleet from reality, they had to exist, so they transported them to the future.