As the issues were framed in Hamdan, the Court had the following options:
1. The Court could have refused to decide the merits on one of several possible grounds. (Justices Scalia, Thomas, and Alito favored this course.)
2. The Court could have said that the relevant statutory provisions and the Geneva Conventions, properly interpreted, authorized the President to try Hamdan in a military commission (and that such trials were constitutionally acceptable). (Justices Scalia, Thomas, and Alito accepted this proposition too.)
3. The Court could have said that the relevant statutory provisions, and the Geneva Conventions, properly interpreted, prohibited such trials -- and that the prohibition of such trials did not unconstitutionally invade the President's power as Commander-in-Chief. (A majority of the Court accepted this proposition for the statutes; for the Geneva Conventions, there was a plurality vote of 4-3 in favor of this proposition, with Justice Kennedy declining to express his view.)
4. The Court could have interpreted the relevant provisions as in 2 above, not only on the basis of their texts, but also by reference to a kind of clear statement principle, requiring unambiguous congressional permission in order for the executive to use military commissions. (No justice explicitly suggested this route.)
5a. The Court could have interpreted the relevant provisions as in 3 above, not only on the basis of their texts, but also by reference to a kind of clear statement principle, saying that if statutes are not clear, the President, as Commander-in-Chief, is entitled to use military commissions. In other words, Congress must speak clearly if it wants to ban the President from using military commissions. (Justice Thomas' opinion, joined by Justice Scalia on this point but not by Justice Alito, veered toward this position without embracing it.)
5b. A variation on 5a: The Court could have said that according to standard principles of administrative law, the President is authorized to interpret the relevant sources of law, so long as his interpretation is reasonable. (Justice Thomas suggested an approach of this kind to the Geneva Conventions issue.)
6. The Court could have said that the President, as Commander-in-Chief, has the authority to create military commissions whatever Congress says. (No justice suggested this route.)
7. The Court could have said that because of constitutional limits, the President may not create and use this kind of military commission, even if Congress authorizes him to do so. (No justice suggested this route, though it is possible that a due process issue could arise with imaginable military commissions.)
The major battle, within the Court, was between positions 2 and 3 -- which gives the opinions their highly technical and mostly dry air. Justice Stevens, author of the prevailing opinion, and Justice Thomas, author of the principal dissenting opinion, wrote carefully and at length, parsing the relevant texts and arriving at opposite conclusions on every major point. A remarkable feature of their disagreement is that it is as if the two sides live, in this case, in parallel legal universes -- by my count, they disagree not on one major issue, or two, or three, but six (a conservative estimate).
To come to terms with the opinions, it would be necessary to go through these debates in detail. To summarize a long story, the prevailing opinion ruled: (1) that a "conspiracy" to violate the law of war could not be tried in a military commission, which was limited, by congressional understanding and longstanding practices, to actual violations of the law of war; (2) that under the Uniform Code of Military Justice, Hamdan must be provided with the same procedural rights as in courts-martial, unless the President made a finding that it would not be "practicable" to provide such rights -- and in this case, the President did not make a sufficient finding with respect to the deprivation of Hamdan's right to see the evidence against him; and (3) that the Geneva Conventions required a trial in a "regularly constituted court" affording guarantees regarded as indispensable by civilized peoples -- requirements that were violated here because the military commission was not "regularly constituted" and the right of access to the evidence against a defendant is a guarantee regarded as indispensable by civilized peoples.
For now, let me simply assert that while the major disagreement seems to be between 2 and 3, it is really between 4 and 5a -- a claim that helps to explain the disagreement on so many questions of statutory interpretation. In other words: Justice Stevens' opinion seems to be animated by the idea that Congress must speak quite clearly if it is going to authorize the President to conduct trials in military commissions. (This is a major departure from Ex Parte Quirin, in which the Court seemed to bend over backwards to find congressional authorization when it was hardly clear.)
In this way, Hamdan seems in line with a long series of cases in which the Court has demanded that the President find unambiguous congressional authorization for an intrusion on civil liberties -- and especially for a departure from ordinary judicial procedures. It is interesting and potentially important that Justice Stevens did not say this explicitly -- but an idea of this kind does seem implicit in the case. There was remarkably little discussion of the President's power as Commander-in-Chief, apparently on the assumption that whatever power he has in this domain, it is legitimately subject to congressional limitations. (See note 23.)
By contrast, Justice Thomas seems to adopt a clear statement principle (of the kind at work in Ex Parte Quirin) to the effect that statutes will be read generously to the Commander-in-Chief, certainly when national security is at risk. Perhaps Justice Thomas believes that if Congress does not speak clearly, and if its enactments can reasonably be interpreted to support executive power, the President, as Commander-in-Chief, has the authority to protect national security. He too does not say this explicitly, but the idea seems to animate his opinion.
Beneath the surface of the technical debate, then, are competing presumptions about how to deal with ambiguous statutory terms. In the long term, the choice of presumption will be extremely important.