From the February 8 edition of Fox News' Fox & Friends:

PERINO: Well, and I -- and the administration continues to tout that during the Bush years, we prosecuted two terrorists, Moussaoui and Reid, like they want to do for Khalid Shaikh Mohammed. And I really want to take a moment just to put that in context. Moussaoui was arrested before 9-11. Reid was arrested six weeks after President Bush first gave the order to do enemy combatant status, and there wasn't a system in place. We're nine years later, and if the only thing they can look back on in the Bush administration to say that was done well was the prosecution of Richard Reid, I would be shocked if that was the case. I'm sure that is not what they believe. And I really think they ought to look at that before they claim that that was the best way to do it. Because I think, arguably, we could have done things better. We just didn't have the system yet. And it was right after 9-11.

Before Reid pleaded guilty, Bush placed hundreds of detainees in military custody

Order Perino referenced stated that military could hold detainees “outside or within the United States.” Reid was captured in December 2001. Bush's November 13, 2001, “Military Order” explicitly stated that “Any individual subject to this order shall be ... detained at an appropriate location designated by the Secretary of Defense outside or within the United States.” The order defined the term “individual subject to this order” as follows:

The term “individual subject to this order” shall mean any individual who is not a United States citizen with respect to whom I determine from time to time in writing that:

(1) there is reason to believe that such individual, at the relevant times,

(i) is or was a member of the organization known as al Qaida;

(ii) has engaged in, aided or abetted, or conspired to commit, acts of international terrorism, or acts in preparation therefor, that have caused, threaten to cause, or have as their aim to cause, injury to or adverse effects on the United States, its citizens, national security, foreign policy, or economy; or

(iii) has knowingly harbored one or more individuals described in subparagraphs (i) or (ii) of subsection 2(a)(1) of this order;

and

(2) it is in the interest of the United States that such individual be subject to this order.

Detainees held by the military as early as November 2001. Soon after the war in Afghanistan began in October 2001, the United States began holding detainees in military custody. For instance, in the 2006 case of Hamdan v. Rumsfeld, the Supreme Court majority opinion stated that in November 2001, the plaintiff in that case, Salim Ahmed Hamdan, “was captured by militia forces and turned over to the U. S. military.”

Padilla transferred to military custody before Reid pleaded guilty in civilian court. Reid pleaded guilty on October 4, 2002, and was sentenced on January 30, 2003. Jose Padilla was initially held in the civilian court system after his arrest on a material witness charge and was transferred to military custody on June 9, 2002. (Padilla was later transferred back to civilian custody for trial after he appealed his detention to the Supreme Court for a second time.)

Hamdi held in military custody since early 2002. In addition to Padilla, Yaser Hamdi was held in military custody at Guantanamo Bay beginning in January 2002 and transferred to a military brig in South Carolina in April 2002.

Hundreds of detainees held in military custody at Guantanamo beginning in early 2002. In the 2004 case of Rasul v. Bush, Justice Stevens, writing for the majority, stated: “Petitioners in these cases are 2 Australian citizens and 12 Kuwaiti citizens who were captured abroad during hostilities between the United States and the Taliban. Since early 2002, the U.S. military has held them -- along with, according to the Government's estimate, approximately 640 other non-Americans captured abroad -- at the Naval Base at Guantanamo Bay.”

Bush administration bragged about handling of Reid

Ashcroft: Reid case an example of “steady progress because of the combined and cooperative efforts of law enforcement and intelligence.” From an August 25 speech by then-Attorney General John Ashcroft:

Around this nation, we can point to quiet, steady progress because of the combined and cooperative efforts of law enforcement and intelligence:

[...]

132 individuals have been convicted or pled guilty, including shoe-bomber Richard Reid, “American Taliban” John Walker Lindh, six members of the Buffalo cell, and two members of the Detroit cell