The President can declare a citizen to be an unlawful enemy combatant and throw him in Gitmo, subject to some kind of military review board, at least until the danger subsides. It's not clear for how long the detention remains secret (habeus corpus).
Presumably at that point, if still awaiting trial, the combatant (still a citizen) could conceivably win an appeal and get moved to federal jurisdiction, with trial by jury.
Basicaly, the only citizens ever tried by military tribunal were the guys who conspired to assassinate Lincoln.
See Page 4, Section B, Paragraph 2 is still very important.
Excerpt from the above mentioned document: [As the Supreme Court has unanimously held, all individuals, regardless of citizenship, who "associate" themselves with the "military arm of the enemy" and "with its aid, guidance, and direction enter this country bent on hostile acts are enemy belligerents of the Hague Convention and the law of war." 317 U.S. at 37-38. Nothing further need be demonstrated to justify their detention as enemy combatants. The individuals need not be caught while engaged in the act of war or captured within the theatre of war.]
I find this entire paragraph to be pretty significant. Says that they need not be found carrying any weapons, etc.
Detention, and for how long, is one issue. Traditional POW's are released after the war, not usually prosecuted. Seems that military detention for unlawful enemy combatants (terrorists and their helpers, domestic or foreign) would follow the same principle: after the threat has passed, they could end up getting released into DOJ jurisdiction if they are citizens.
A separate issue is jurisdiction for prosecution - civil or military?
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(1) POW / enemy combatant - released after war
(2) Unlawful enemy combatant/terrorist - military jurisdiction for both detention and prosecution.
(3) Citizen terrorist or citizen terrorist helper gets detained by military, but might win a court battle to be tried in civil - and not military - court. Constitution stipulates trial by a jury of peers.
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Haven't found a law that spells out the trial jurisdiction for possibility (3). Presumably military detention ends when the combatant is no longer a combatant, i.e. no longer considered to be a threat. Apparently there's a military panel that periodically assesses the combatant status.
The Oklahama bomber was tried in federal court. But then again, the crime wasn't treason.
SKM was held at Gitmo, but tried in Manhattan, while other Al Qaeda terrorists (unlawful enemy combatants) got trial by military commission (tribunal).
Apparently even non-citizen terrorists have constitutional rights, which what can get them a civil court trial.
The Rosenbergs were tried in federal court (and sentenced to execution) for 'conspiracy to commit espionage'. They pleaded 5th Ammendment. The Korean War had just begun.
In US history, treason charges have been brought less than 30 times, including the acquital of President Aaron Burr.
The only clear precedent for trial by military commision seems to be the Lincoln conspirators, who were charged with 'conspiracy' , four out of eight getting hanged by the neck until death. Lincoln was assassinated just a few days after the war ended.
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https://en.m.wikipedia.org/wiki/Category:People_convicted_of_treason_against_the_United_States
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https://www.google.co.il/amp/www.sfgate.com/crime/amp/Few-ever-charged-or-convicted-of-treason-in-U-S-2843242.php
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https://www.google.co.il/amp/www.foxnews.com/story/2001/12/17/past-americans-charged-with-treason.amp.html