Angelsboi, you have to understand that it will be difficult to impossible for someone on this board to help you flesh out what looks like an entire game session for you. Many of us have our games to run and can only afford a few suggestions or nudges in the direction we individually think is best.
Right off the bat:
Why is this player not interested? Does he feel railroaded? Does he feel like he has no input into the process? Does he feel that it does not suit the character? Are there real life issues playing with his mood come game time?
If you have the option: switch players. Player A may not be grooving on the plot, but Player B may be very excited. You could always claim that A was actually a feint, meant to confuse the opponent.
If the players just decide to pull out of the subplot, as others suggested let it run its course without the interference of the PCs. Stuff happens, right? If the PCs could have stopped it, they will share some of the blame.
That said, I think you are trying to push your games into too much of a television show. This may or may not be working for your players - ask them and see. If it is, then maybe you are either not planning enough (like the lack of a game structure for the Chess game, something I would think would be integral to this plot line), or are planning yourself into a corner.
And never bet on what the PCs will do, either.

I see in the link that you are assuming the PCs (IIRC) were going to flee the site. Who knows? What if they decide to disguise themselves and stick around to see what happened. What if they decide to turn themselves in? What if they decide to fight there way out? Contingency plans are important and if you aren't letting your PCs have options of what they can do next, it may be taking the life out of their enjoyment and may explain why your player has opted out of this plotline.
Ashtal