The charge of Colonel Jackman's Missouri Cavalry had finally washed over the line of the 2nd. KSM after 45 minutes of battle, leaving Topeka Battery the last intact fighting force from the 2nd. on the field. Although the outcome of the battle had been decided, Captain Ross Burns fought on with his pistol before he was finally smashed over his head with the butt of a Rebel carbine and the remainder of his battery surrendered. Survivors recall hearing Confederate officers in the vicinity ordering their men not to kill the Captain of the gun. Topeka Battery suffered the highest losses of any Company of the 2nd. - every man was either killed, wounded, or taken prisoner.
After the men of the 2nd. were driven back to the Big Blue River by the Rebel charge, an attempt was made by Lt. Colonel Greene to rally them for the purpose of forming another line. Captain Huntoon of Company B realized the futility of such an action as they were completely surrounded by Rebels and suggested to Lt. Col. Greene that they had better surrender, and he gave the order to do so. After Col. Jackman's men collected their arms and ordered the Kansans to dismount it became clear that they intended to take prisoners only after killing the officers in charge: Lt. Col Green was stripped of his clothing and shot three times before he fell into the underbrush. Captain Huntoon made an attempt to escape this fate by making a dash on his horse but was recaptured near the battle-site and had to convince a young Rebel not to let his comrades commit murder. As Captain Huntoon was lead over the battlefield toward Rebel headquarters he noticed the body of Ben Hughes, the driver of one of the wagons. His throat had been cut ear to ear which was not a battle wound; Ben Hughes was black. They now passed the Battery and beside the Gun lay Dan Handley still writhing in spasms which often follow mortal wounds; further on in the lane lay dead and dying men and horses as the result of double canister fired at close quarters.
While Captain Huntoon was being lead toward Rebel Headquarters, the bulk of the prisoners from the 2nd. had been rounded up and were brought back to where the gun stood in the lane. They were aligned in a row and opposite each man was a mounted Rebel holding a revolver. An eyewitness to this incident was Guilford Gage of Topeka Battery and he later stated that these Rebel captors who awaited the final order to fire were not Confederate Regulars but of the type known as Border Ruffians: savage men who committed atrocities in the name of revenge, the original cause being lost to memory. There was plenty of this type on the Federal side as well but that was of no matter to Gage and his comrades, they only knew that in a moment they would all be dead. As the final moment neared, the sudden appearance of General Shelby between the two lines prevented the mass execution and with extremely terse language he ordered the prisoners over to the guard of his own veterans. While Shelby was a fine General and an honorable man, he would have to live with this element of the Rebel Army for the remainder of his duty in Missouri. As for the men of the 2nd., if they knew the travails that awaited them, they may have wished for the quick end to their suffering that execution would have given.