What if Trump orders Mattis to do something deeply unwise?

If a disagreement arises between the President and the Secretary of Defense, the President’s view, and whatever orders stem from that view, carry the day. The uniformed leadership then has to either comply or risk being relieved of command and court-martialed in accordance with Article 92 of the Uniform Code of Military Justice. As Colonels Reeves and Wallace explained, these duties of uniformed officers only apply to lawful orders. But the ultimate legality or not of the order might be finally resolved only if there is a court martial under Article 92. And in the meantime, the President could fire a uniformed officer for failing to carry out an order that the officer believed was unlawful. (There is a tricky question as to whether Secretary Mattis, as a retired military officer entitled to pay, is subject to the UCMJ under Article 2(a)(4) and thus bound by its duties and subject to court martial for not obeying a lawful order of the Commander-in-Chief. We do not pursue this matter further because whether he is subject to the UCMJ or not, Trump could fire him for disobeying an order in any event.)

Contrary to these principles, by some accounts, President Nixon’s Secretary of Defense James Schlesinger ordered General George S. Brown, Chairman of the Joint Chiefs of Staff, not to execute Nixon’s orders without checking with him, or (in a different version) ordered military commanders to “check with either him or Secretary of State Henry Kissinger before executing” a nuclear launch order from Nixon.