Arresting and sending all of Congress to Gitmo will immediately collapse the stock market. It would be the biggest/fastest drop in history. Probably drop 95% overnight.
There would be mass riots and civil unrest like never seen before, power blackouts, food shortages, looting, etc.
If it happens, its going to look like Armageddon for a while so if you really believe he's going to arrest nearly the entire government be prepared and stock up on food/water.
FEMA would run the country. FEMA is designed to run NCP (National Continuity Programs) Yes, the stock market probably would crash. That's why I've selling off my portfolio for two weeks now and not buying back hardly anything. https://www.fema.gov/about/offices/continuity