[ . . . ] abstention is not appropriate in cases in which individuals raise "'substantial arguments denying the right of the military to try them at all,'" and in which the legal challenge "turn[s] on the status of the persons as to whom the military asserted its power."The case cited involved the court martial of a pot-dealing US Army officer, and therefore no questions of jurisdiction were raised. The court found that the effective function of Armed Forces discipline was predicated on the operation of courts-martial, and therefore it would be disruptive to that discipline for the regular court system to insert itself into those operations before they had been resolved.
Scalia's response to this majority finding opens on a "respectfully-disagree" note (on page 121):
Admittedly, Councilman does not squarely control petitioner's case, but it provides the closest analogue in our jurisprudence.He then goes absolutely bat$#!+ insane (on page 122):
To put this in context: The charge against the respondent in Councilman was the off-base possession and sale of marijuana while he was stationed in Fort Sill, Oklahoma [ . . . ] The charge against the petitioner here is joining and actively abetting the murderous conspiracy that slaughtered thousands of innocent American civilians without warning on September 11, 2001.The rationalization for inserting this bit of raw emotionalism into a legal argument? Scalia is using the comment to preface his argument that military tribunals are implicitly included in the definition of "all necessary and appropriate force" as authorized by Congress against anyone involved in the execution of the 9/11 attacks. Thomas, in a separate dissent, restates this argument, and points (on page 130) to precedents indicating that tribunals are an inherent part of war, going on to argue that for the Court to review a claim by a detainee in military custody constitutes an intrusion on the President's authority to conduct war. This argument seems to parallel the aforementioned assertion that Guantanamo is not under US control -- in essence, Thomas is arguing that the President's assertion of unilateral control is acceptable under a claim of "military necessity" because the circumstances don't permit judicial review. (This is a fascinating argument for a Justice to include in a decision on the merits of a case under review.)
Stevens also (on page 31) points to a case in which German infiltrators were apprehended on US soil and the President established a tribunal to handle the case. In that case, the Court convened a special term specifically to examine the infiltrators' petition while the tribunal was ongoing. Scalia counters that in that case, there was no appeals process or review mechanism in place for the tribunal's decision, whereas in the present scheme judicial review is possible after the tribunal's decision is rendered.