Lincoln delivered a message to the special session of Congress.[5] He referred to his suspensions of the writ, quoted the suspension clause, and justified the suspensions on the ground that "we have a case of rebellion, and the public safety does require" suspension of the writ. He then went on: "Now it is insisted that Congress, and not the Executive, is vested with this power. But the Constitution itself, is silent as to which, or who, is to exercise the power; and as the provision was plainly made for a dangerous emergency, it cannot be believed the framers of the instrument intended, that, in every case, the danger should run its course, until Congress could be called together; the very assembling of which might be prevented ... by the rebellion. No more extended argument is now offered, as an opinion ... will probably be presented by the Attorney General. Whether there shall be any legislation upon the subject, and if any, what, is submitted entirely to the better judgment of Congress."[6]

The promised opinion of Attorney General Edward Bates came the next day.[7] The opinion was devoted primarily to the president's power to make arrests without warrant, rather than to the suspension of habeas corpus. Bates argued that the president is authorized to suspend the writ because he is charged with preservation of the public safety, but he then concluded with his personal opinion that the power of suspension flows from the president's power to make warrantless arrests.

While Lincoln's defense of his constitutional power of suspension is stated tentatively in his message to Congress, his actions and later words confirm his belief that he, and he alone, had the constitutional power to suspend the writ of habeas corpus.

On July 2, just two days before Congress convened, Lincoln issued an order authorizing suspension of the writ of habeas corpus between New York and Philadelphia—friendly territory for the administration. But he didn't suspend the writ, which suggests a lack of urgency. Lincoln could have sought and almost certainly could have obtained congressional authorization before issuing the order, but he didn't do so. He didn't seek suspension authorization in his July 4 message or at any later time. Indeed, when he says in his message that "whether there shall be any legislation on this subject ... is submitted to the better judgment of Congress," Lincoln appears to advise Congress to act with more deliberation than speed if it decides to act at all.

Congress accepted Lincoln's invitation to dawdle. As we will see, Congress did not enact legislation authorizing suspension of habeas corpus until March 3, 1863. In the meantime, Lincoln's 1861 orders authorizing suspension remained in force, and on September 24, 1862, he issued a proclamation imposing martial law and suspending the writ of habeas corpus. The proclamation orders that, for the rest of the war, (i) "all rebels and insurgents, their aiders and abettors within the United States, and all persons discouraging volunteer enlistments, resisting militia drafts, or guilty of any disloyal practice, affording aid or comfort to rebels against the authority of the United States, shall be subject to martial law and liable to trial and punishment by courts martial or military commission," and (ii) "the writ of habeas corpus is suspended in respect to all persons arrested or imprisoned in any fort, camp, arsenal, military prison, or other place of confinement by any military authority or by the sentence of any court martial or military commission." [8]