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.
I think he survives because it would be too profitable for him to make some 24 Bauer movies.
If you get the PS2 game, or read the storyline for the game online, you will find that the game answers some of those questions about who was behind season 2.
You're assuming the writers have some sort of master plan to tie all of these seasons together, when they don't even have a master plan for each individual season.
SD