X-Men: Everything You Need To Know Before Marvel's Big Relaunch
3. Mr. Sinister Is Missing
For the latter half of Rosenberg's run on Uncanny Mr. Sinister maintained a decent presence - either fighting against the X-Men or interacting with Emma Frost following his capture.
Yet, while attempting to help Wolverine recover from some injuries, Logan quickly sliced up the villain and it was then revealed that the version of Sinister that had been seen throughout the series was actually a clone all along - meaning that the real one is still out there somewhere.
This, along with Sinister's obvious history with cloning, may play into the 'birthing' of that Cyclops and Jean Grey in very first pages of House Of X - though that could also very easily just be Xavier being a jerk, something which will be explored in a later entry.