He was first buried in Kentucky, but his mother wanted to bring him home to Canal Dover, Ohio. She hired one of his boyhood friends to help her get the remains moved. By the time they got around to this, the remains were skeletal or mostly skeletal. The coffin had deteriorated, and collapsed, leaving small fragments of bone in the original grave. The rest was reboxed for shipment to Ohio--except the friend wasn't very honest with Mrs. Quantrill. He kept the skull and most of the long bones. A coffin containing some of Quantrill's skeleton was buried in Dover. Later, the friend peddled the long bones to a Kansas collector. I believe this was William Elsey Connelley, the Kansas historian. In any event, they eventually came into his possession. Quite some time later, he gave them to the Kansas Historical Society and they were displayed in a glass case for a long time. The collector wasn't interested in the skull, though, so the boyhood friend kept it the rest of his life. His son "inherited" it, and used it initiation rituals in his fraternity. This went on for years, until the fraternity chapter went inactive. At that point the skull was finally buried with the rest of the Dover remains. It is in a child's coffin, buried about three feet deep over the main Dover coffin. Cemetery officials were reluctant to dig any deeper, for fear of disturbing the coffin below.
Meanwhile, back in Kansas, all of the Native American bones in museums and labs were repatriated as much as possible to their tribes, or otherwise reburied. The Kansas State Historical Society decided to divest themselves of Quantrill's long bones, too, so they made preliminary arrangements to send them to Dover. However, a Confederate group (probably the William Clark Quantrill Society) made a counter proposal. Quantrill's first Dover funeral had been held in secret and the grave was unmarked. The Society thought he deserved better and proposed a military funeral in the Confederate Cemetery in Higginsville. That was done with Confederate pall bearers, flag waving, rifle salutes, etc. They specifically did NOT include cannon salutes because, as they said: "Whenever cannons are at a press event, the cannons are the only thing that appear in the local newspaper." Quantrill's Missouri coffin was covered by several bags of cement mix before the grave was filled, so that seeping rain would eventually harden it and create a deterrent to grave robbers.
I believe the skull was the last piece of him to be buried and now his Dover grave is marked, too.