Cross-referencing: National Security Law (NSL), Ch. 14, pp.541 et seq.; Ch. 2, p.32.
Laws may not silent in times of war, but the Charter is (at least if the war is a foreign one). At core, this is the implication of the Federal Court of Appeal's December 2008 decision in Amnesty International v. Minister of National Defence. The Federal Court of Appeal upheld a Federal Court decision, a judgment discussed elsewhere in this blog. It did so based on a reading of the Supreme Court's decision in Hape that seems impossible to defend in light of that Court's further decision in Khadr.
In my view, Hape and Khadr stands for the following proposition: absent consent by the foreign state, the Canadian Charter of Rights and Freedoms does not attach to the overseas actions of Canadian officials except where those actions are contrary to Canada's international obligations (and more specifically, its international human rights obligations). The threshold question is, therefore, whether the Canadian officials are acting in compliance with Canada's international human rights obligations. If they are not, then the Charter applies.
The analysis that should have been undertaken by the Federal Court of Appeal concerns, therefore, the scope of Canada's international human rights obligations in relation to Canadian Forces practices on Afghan detainees. There, the inquiry must focus on the reach of instruments such as the International Convenant on Civil and Political Rights, the Convention Against Torture -- and there is a jurisprudence on the Covenant in particular that discusses the extraterritorial reach of human rights obligations to state agents acting beyond their borders -- international humanitarian law, and the issues of lex specialis that governs the interaction between this international humanitarian law and the aforementioned human rights treaties. The question of "effective control" by the CF of Afghan territory, which has appeared in the Federal Court case as a separate ground for asserting the application of the Charter, is not a separate ground. Instead, "effective control" is a short-hand for the test developed in the international jurisprudence to decide when the Covenant reaches the extraterritorial actions of states bound by it.
So, in sum, here is the analysis: The Charter applies if Canada's international human rights obligations apply. Canada's international human rights obligations apply either because some norm of international human rights or humanitarian law reaches the conduct of the CF in Afghanistan. Humanitarian law obviously does -- the Geneva Conventions and their customary equivalents attach to the armed conflict and extend georgraphically to the entire theatre of conflict. Human rights law may, (a) so long as it is not displaced by the lex specialis of IHL (and, in a case concerning conditions of detention and treatment, there likely isn't any displacement, in my view -- lex specialis requires a contradiction between the two areas of law, not just overlap) and (b) so long as on the face of those treaties (and customary norms) which govern human rights law, there is extraterritorial reach. On the latter point, the question then terms to the level of control exercised by the CF.
The Federal Court of Appeal, however, launches down a path of its own, denying that Hape and Khadr mean much at all when it comes to tying the Charter to Canada's international obligations. Its most puzzling statement is this one: "I understand the Supreme Court of Canada to say that deference and comity end where clear violations of international law and fundamental human rights begin. This does not mean that the Charter then applies as a consequence of these violations." But what else could the following statement from the Supreme Court in Khadr possibly mean:
 In Hape, however, the Court stated an important exception to the principle of comity. While not unanimous on all the principles governing extraterritorial application of the Charter, the Court was united on the principle that comity cannot be used to justify Canadian participation in activities of a foreign state or its agents that are contrary to Canada’s international obligations. It was held that the deference required by the principle of comity “ends where clear violations of international law and fundamental human rights begin” (Hape, at paras. 51, 52 and 101, per LeBel J.). The Court further held that in interpreting the scope and application of the Charter, the courts should seek to ensure compliance with Canada’s binding obligations under international law (para. 56, per LeBel J.).
 If the Guantanamo Bay process under which Mr. Khadr was being held was in conformity with Canada’s international obligations, the Charter has no application and Mr. Khadr’s application for disclosure cannot succeed: Hape. However, if Canada was participating in a process that was violative of Canada’s binding obligations under international law, the Charter applies to the extent of that participation.
A search and replace of para 19 would read:
If the detention process under which Afghan detainnes are being held was in conformity with Canada’s international obligations, the Charter has no application and the Afghan detainee's application for Charter relief cannot succeed: Hape. However, if Canada was participating in a process that was violative of Canada’s binding obligations under international law, the Charter applies to the extent of that participation.
It should be as simple as that. We'll see what the Supreme Court does on appeal.