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... but the rest of that section contains no references limiting its applicability to Congress, which strongly suggests that those restrictions apply to all branches of Congress (and arguably to individual states as well).

Article I, section 8 enumerates the delegated powers to the federal legislature, section 9 enumerated the powers prohibited to the federal legislature, and section 10 enumerates the powers prohibited to the states. In Article II it is found that, "[t]he Congress may determine the Time of chusing the Electors", so would you maintain that Congress may execute Presidential powers of appointment and serve as commander-in-chief, simply because that branch is also mentioned in Article II?

This last statement makes it clear that Taney either lacked the courage of his convictions or (more likely) was just making his latest attempt to please his Confederate friends.

Ya think? Consider what Chief Justice Roger B. Taney wrote in ex parte Merryman about the suspension of the writ of habeas corpus - first he cited Justice Story, "[i]t would seem, as the power is given to congress to suspend the writ of habeas corpus, in cases of rebellion or invasion, that the right to judge whether the exigency had arisen must exclusively belong to that body".

Next he cited former Chief Justice John Marshall, "[i]f at any time, the public safety should require the suspension of the powers vested by this act in the courts of the United States, it is for the legislature to say so."

Then the Chief Justice adds his opinion, "[t]his article is devoted to the legislative department of the United States, and has not the slightest reference to the executive department." He notes that the Constitution directs that all legislative powers shall be vested in congress, and that the powers of the President are limited to enumerated powers in Article II, "[a]nd if the high power over the liberty of the citizen now claimed, was intended to be conferred on the president, it would undoubtedly be found in plain words in this article; but there is not a word in it that can furnish the slightest ground to justify the exercise of the power."

Next he asserts that the Constitution cannot be suspended, "[n]or can any argument be drawn from the nature of sovereignty, or the necessity of government, for self-defence in times of tumult and danger. The government of the United States is one of delegated and limited powers; it derives it existence and authority altogether from the constitution, and neither of its branches, executive, legislative or judicial, can exercise any of the powers of government beyond those specified and granted; for the tenth article of the amendments to the constitution, in express terms, provides that 'the powers not delegated to the United States by the constitution, nor prohibited by it to the states, are reserved to the states, respectively, or to the people."

How much plainer can he be? He cited two other legendary justices, along with his own opinion about the legality of the President's actions. He is quite candid in his assessment:

"These great and fundamental laws, which congress itself could not suspend, have been disregarded and suspended, like the writ of habeas corpus, by a military order, supported by force of arms. Such is the case now before me, and I can only say that if the authority which the constitution has confided to the judiciary department and judicial officers, may thus, upon any pretext or under any circumstances, be usurped by the military power, at its discretion, the people of the United States are no longer living under a government of laws, but every citizen holds life, liberty and property at the will and pleasure of the army officer in whose military district he may happen to be found."
"In such a case, my duty was too plain to be mistaken. I have exercised all the power which the constitution and laws confer upon me, but that power has been resisted by a force too strong for me to overcome."

Since Chief Justice Taney is not the Commander-in-Chief, he certainly can't order the miltary to arrest Lincoln. Isn't the President required to abide by judicial decisions, or is he above the law?

In Article II it is found that, "[t]he Congress may determine the Time of chusing the Electors", so would you maintain that Congress may execute Presidential powers of appointment and serve as commander-in-chief, simply because that branch is also mentioned in Article II?

No, because Article II specifically calls for the President to be Commander in Chief and appoint Ambassadors, etc. with the advice and consent of the Senate. In contrast, the habeas corpus provision of Art. I, Sect. 9 is ambiguous because the passive voice is used therein with no with no indication as to whether it is referring to Congress, the President, the Judiciary, or the government of a state. Your suggestion that Section 9 merely "enumerated the powers prohibited to the federal legislature" is therefore presumptive. As a well trained lawyer, Lincoln knew to never to presume anything about the law. The burden was on anyone who objected to his interpretation to properly challenge it. If you assume as you have that Lincoln was usurping the role of Congress, it was imcumbent upon Congress to formally state their objection thereto through some sort of resolution or bill. They not only failed to do so, they in fact ratified Lincoln's suspension of the writ of habeas corpus.

Consider what Chief Justice Roger B. Taney wrote in ex parte Merryman about the suspension of the writ of habeas corpus - first he cited Justice Story, "[i]t would seem, as the power is given to congress to suspend the writ of habeas corpus, in cases of rebellion or invasion, that the right to judge whether the exigency had arisen must exclusively belong to that body".

Are you arguing that Lincoln was bound by what a (even highly reputable) jurist wrote in a mere commentary? I'm not saying that no reasonable person would suggest that suspension of habeas corpus was intended to be an exclusive proivince of Congress. My main point is that Lincoln had a plausible argument for his decision to suspend habeas corpus, and any attempt to brand him "a dictator" or "the American Lenin" for doing so is ridiculous given that (a) the issue was (and remains) unsettled law and (b) Congress ratified his action. Moreover, Taney certainly didn't aquit himself well as a jurist by making his blatantly flase statement about Article I having "not the slightest reference to the executive department."

Having briefly reviewed Ex parte Bollman and Swartwout, it appears that the portion quoted by Taney is mere dictum, since the President had not suspended habeas corpus in those cases. Marshall was merely holding that the Court had the Constitutional/common law authority to issue a writ of habeas corpus even in the absence of statutory authorization from Congress. Note that Marshall doesn't say even in dictum that the President is prohibited from suspending habeas corpus.

Then the Chief Justice adds his opinion, "[t]his article is devoted to the legislative department of the United States, and has not the slightest reference to the executive department." He notes that the Constitution directs that all legislative powers shall be vested in congress, and that the powers of the President are limited to enumerated powers in Article II

Do you agree with Taney that Article I "has not the slightest reference to the executive department" and "the powers of the President are limited to enumerated powers in Article II"? (Hint: Before you answer this question, please read Section 7 of Art. I and note that Art. II does not grant the President any power to sign or veto Congressional bills or resolutions.)

"[a]nd if the high power over the liberty of the citizen now claimed, was intended to be conferred on the president, it would undoubtedly be found in plain words in this article..."

Isn't is equally (in)valid to state that "if suspending habeas corpus was intended to be the sole province of Congress, it would undoubtedly be found in plain words in Article I"?

How much plainer can [Taney] be?

Taney was plain enough -- it's just that his plain words don't amount to a convincing argument that Lincoln was wrong (let alone that he was "the American Lenin").

I can only say that if the authority which the constitution has confided to the judiciary department and judicial officers, may ... upon any pretext or under any circumstances, be usurped by the military power, at its discretion, the people of the United States are no longer living under a government of laws, but every citizen holds life, liberty and property at the will and pleasure of the army officer in whose military district he may happen to be found.

True enough perhaps, but in arresting Merryman, the military was not acting on its own in peacetime -- they were acting pursuant to (at least arguably) Constitutional Presidential authority during a massive rebellion which imminently threatened the Capital city and all of its inhabitants.

Since Chief Justice Taney is not the Commander-in-Chief, he certainly can't order the miltary to arrest Lincoln. Isn't the President required to abide by judicial decisions, or is he above the law?

Any interested party who objected to Lincoln's refusal to obey Taney's Circuit Court order could have sought relief from the Supreme Court and/or Congress. I am not aware of any such objection being pressed through the Constitutionally provided channels.