My point is that the twist is that they are not extinct after all, yes?
But if this saturday's episode is, as it seems to be, back on the station where Simon Pegg was the bad guy, that dates the episode to 200000 AD, yes?
Now, as Harkness says he thought they were extinct too, and he is from the 51st century, then if they were already thought extinct by then, then not turning up until the year 200000 is a bit of a long time to be out, yes?
Yet Harkness also recognises their ships. Which therefore leaves the three possibilities I left above.