Here's what I've surmised about what went down from other sources--Fox was on the verge of cancelling the series after season four. In fact, the season four finale had two different endings shot, one to close out the series for good, the other (which we saw) to setup the coming of the Observers and season five. But Fox relented due to some last minute calculating by the bean counters due to the series needing another 13 episodes to get to that special 100 episode mark which would pay back the most on syndication rights. So we get 13 more episodes; not a full 22 episode order but at least we are going to get some kind of closure (I hope).
Great setup for the next three hours that is for sure. I am going to miss this series when it leaves. It has been brilliant television.