Tony is dead.
"No, get me an oitment, I can still make it I tell ya!"
The "Pandora's Box" that Henderson is talking about has to be some kind of conspiracy that goes up to the highest levels of the U.S. government. It has been going on for some time and has tentacles into everything. Nina Myers was involved (remember she told Jack before he capped her that she still had "valuable information") although Walt Cummings was just a pawn and didn't realize it. The nuclear bomb plot in Season Two was part of it (remember who was actually behind it) and the events of Season Four were being manipulated by someone we never saw but Marwin referred to as "The Emir".
When the series ends, probably next year, my prediction is that Jack will die at the end but in the process bring down the traitors.