Maj. Julius C. Fisk of the Second Kansas Volunteers replaced Capt. Whittenhall on August 5th. He was only in command a few weeks before Capt. H.N.J. Reed of the Ninth Kansas Volunteer Cavalry took over as post commander on August 20th.
Capt. Whittenhall's actions in changing the Indian annuity distribution from Fort Lyon to Fort Larned had placed the fort in grave danger. Hundreds of Indians had flocked to the area and when Col. Leavenworth arrived the fort was surrounded by Apache, Arapaho, Cheyenne, Kiowa and Comanche in camps waiting for their goods and annuities. Col. Leavenworth, along with the Indian Agent, S.G. Colley, held meetings with the various chiefs and convinced them to return to their own lands to wait for the annuities.
By October 20th, Lt. Col. Charles S. Clark of the Ninth Kansas Volunteer Cavalry had been placed in charge of Fort Larned by Col. Leavenworth. There is little information about his tenure, although one consequence of the Indian scare brought about by Whittenhall's actions was a rise in troop levels at the fort to almost full strength. By November there were eight companies at the post from five different regiments—Second U.S. Infantry, First Colorado Volunteers;Ninth Kansas Volunteers, Ninth Wisconsin Artillery battery—for a total of 494 enlisted men and 16 officers.
By December 3rd, Capt. Jacob Downing of the First Colorado Volunteers had replaced Lt. Col. Clark as post commander. He was soon replaced by Lt. William West of the Second U.S. Infantry on December 16th, who finished out the year as the fort's 6th commanding officer in as many months.
The latter half of 1862 was a tumultuous time for Fort Larned. The succession of post commanders disrupted the command continuity and the near disaster brought on by Capt. Whittenhall's change of the Indian annuity distribution had placed the fort in very real danger of being overrun by Indians. However, this was only a preview of things to come for the remainder of the Civil War years. With intensified fighting in the East Confederate forces would actively try to bring the Plains Indians to their cause in an attempt to disrupt Union hold on these frontier posts.