Okay, so I've been keeping up with the latest Cover Story, and I have come to 2 possible outcomes to 'WHY' the Marines are now 'attacking' or whatever you want to call it CP9.
1. Spandam took initiative to turn the story into "CP9 allowed the pirates to invade" and thus they are responsible, and now the Marines are searching for them to administor punishment on CP9 or to re-gather them for interrogation and release appropriately.
2. More Interesting.. They are gathering them to help Guard Fire Fist Ace at the Execution Platform.. After-all, CP9 is the only Assassin group for the World Government, probably the only group of 'strong' individuals that can blend in with the crowd and not be known as 'Government' unlike the Admirals and Shichibukai.. I think, perhaps, this reason is turning out to be more likely because of the timing of its entry to the chapters..
Thoughts?