When Confederate troops under the command of General Nathan Bedford Forrest poured into Fort Pillow, Hunter joined Sgt. Ben Robinson, Charlie Key, Sandy Cole, and Aaron Fentis, all Negro survivors of Company D, in a small cluster and fought the Confederates as they came. They were able to keep the attackers at bay for a time, but it was soon clear that as the Confederates kept pouring in, the fort was done for. The group fled to the banks of the Mississippi River, where the found stores of ammunition placed on the river by Major William Bradford before the battle began in earnest. As the group began reloading their weapons, they saw Confederate troops were firing on the USS New Era, a ship that had been providing artillery cover during the battle, and was supposed to be covering the retreat of the garrison. Confederate sharpshooters were not letting the gunners open up their hatches. Finally, the New Era steamed up-river.
Things went from bad to worse for the group, as each were injured in turn, although none were fatally so. Hunter himself was shot in the buttocks. Ultimately, the group was evacuated with the rest of Fort Pillow's defenders.