When a Confederate force under Col. Douglas H. Cooper attacked Unionist tribes in the Indian Territory, Mikko aligned his followers with Opothleyahola's Upper Creeks and resisted.
Together, they fought Cooper in a series of losing battles in the winter of 1861–62 that led to the withdrawal of the Union sympathizers to Kansas in a bitter trek known as the "Trail of Blood on Ice."
Mikko formally enlisted in the Union Army as a captain in May 1862 and was assigned command of Company A of the First Indian Home Guards.
The First Indian Home Guards arrived on the battlefield, dismounted, and entered a patch of woods on the left-center, flanked by two white regiments from Kansas and Iowa.
"[3] Eventually being reassigned to command of Company F, Billy Bowlegs remained prominent in the fighting in Kansas and Indian Territory.