** Paragraph #2: Why is "holiday season" in quotation marks? It is what it is -- Christmas IS a holiday season, and even a Muslin would recognize that. He wouldn't observe the holiday, but rather than put it in mental quotation marks, he would likely just think of it as a Christian holiday -- as we Christians think of ramadan as a Muslim holiday.
Also, it's unlikely that a Muslim would be listening to Christmas music.
** "Once logged into the VPN, he sent an e-mail to his brother warriors around the world. The e-mail itself was also encrypted with another free software program; double encryption was standard procedure, and much more rigorous than what even the American special forces used in their hunt for the Sheikh."
Grammatically incorrect/redundant. It should be either "... The e-mail itself was encrypted with another free software program; ..." or "... The e-mail itself was also encrypted with a free software program; ..."
** "The neatly wrapped paper package was marked as a biohazard. He peeled back the paper to reveal a fiber box, and inside it, a gleaming aluminum case. Within it he found the delivery he had long expected.
He rolled up his shirt sleeve. The metal syringe was cool to the touch...."
So the reader is left to divine that the gleaming aluminum case contained a syringe? IMHO (as an editor of many years), one does not speak of "the" anything when the anything has not been previously introduced to the reader.
** "He pushed on the plunger and saw a tiny drop of the contents emerge from the needle, and without hesitation, jammed the needle into his arm. It was his duty, his shahida."
Move the comma: "He pushed on the plunger and saw a tiny drop of the contents emerge from the needle and, without hesitation, jammed the needle into his arm. It was his duty, his shahida."
** In general, I think you're trying to develop too many parallel story lines at once, and I think you're being overly transparent about the GUNZ! Also, IMHO you have too many lines going about people who are prepared, or at least prepared to prepare. Such are the minority, as Katrina demonstrated. Where are the story lines about the people and families in "Condition White"?