Major A.V.E. Johnston and the 39th Missouri Infantry, which had been tracking the Confederate guerrilla force of Bill Anderson, et al, were attracted to Centralia by the smoke from the burning engine and depot, arriving a couple of hours after the Union prisoners who had been taken off of the train had been executed. The Battle of Centralia, and the Centralia Massacre, both occurred on the same day, only a few hours apart. After Major Johnston arrived in Centralia and had seen the carnage, he was soon moving his men of the 39th Missouri Infantry out of town and into the countryside to seek revenge on the guerrillas for those executions. As he was moving toward his fate, an engineer got the burned out train engine running, loaded it with civilians, and headed it up the rail line to Sturgeon. As the engine was taking on fuel in Sturgeon, the first of a handful of survivors from Johnston's now-destroyed force arrived there, and related the story of the disaster that had befallen Johnston. Shortly afterward the train proceeded on to Renick, where Lt. Col. Dan Draper and a portion of the 9th Missouri State Militia Cavalry were present. Upon hearing the sketchy second-hand account of what had transpired, Draper telegraphed the outside world and headed toward Centralia.
With the news going out over the wires, word quickly reached Col. David Patterson Dyer, who was visiting in St. Charles. Dyer immediately commandeered a train, and stopped off in Mexico, MO., long enough to gather two companies of his command, the 49th Missouri Infantry, that were stationed there. While Dyer was in Mexico, Congressman James Rollins, who had been present in Centralia during the massacre and subsequent battle, arrived in town and provided Dyer with a more thorough report of what had happened. In providing the detailed account to Dyer, Rollins elicited a promise from Dyer not to burn Centralia after advising him that the citizens there had no hand in what had happened.
With his troops, Dyer boarded the train and was the first Federal to arrive in Centralia in the aftermath of the events there. Dyer's infantry were no better armed than Johnston's had been, and were not mounted. Consequently, Dyer chose to remain only long enough to gather up the three dozen or so dead Union soldiers in town and load them onto the train before returning to Mexico where he buried them in a mass grave in the Old Cemetery. The following day Dyer's troops captured two men purported to be Centralia Confederates, interrogated them, paroled them, and buried them. Paroled is a quote from a Federal report of the day.
Lt. Col. Dan Draper and the 9th Missouri State Militia Cavalry entered Centralia a few hours after Dyer had left and had the remaining 100 plus Federal bodies brought in from the countryside. Draper had the Centralia citizens dig a mass grave in town, where he buried the troopers of the 39th Missouri Infantry, with the exception of just a handful who were taken away by family members.
Major A.V.E. Johnston was one of the handful not buried at Centralia. He was taken to Monroe City where his grave is easily located in a family plot at St. Jude's Cemetery. Colonel Draper hailed from a very prominent Pike County Radical family; Colonel Dyer was a very prominent Pike County Radical; Major Johnston was an officer in the Pike County Radical political organization. No doubt they were all very well acquainted with one another, thus ensuring Johnston being one of the very few Centralia Federal casualties to be interred in his own grave.
Afterward, the bodies in Mexico and Centralia were disinterred, and were transported to Jefferson City where they were buried in a mass grave in the National Cemetery. There is a monument over the gravesite listing the names of ALL the Federals killed at Centralia. This listing includes Johnston's name, and is sometimes mistaken to be a listing of the men who rest under the monument. I butted heads several Centralia historians on this issue, finally convincing them after directing them to an obscure primary source reference regarding the disposition of his remains, and actually physically locating Johnston's grave in Monroe City.
I would note that in regard to the remains of the few individuals that were taken away from Centralia by family members, that it was probably done so while the remains were fresh. As stated, the mass grave there contained the remains of around 100 men. It would be tough to recover one or two individuals once the grave was closed, and equally hard to identify specific individuals once it was reopened a few years later.
Sources: Official Records, Ser. 1, Vol. 41, Pt. 1, pp. 417, 441; O.R., Ser. 1, Vol. 41, Pt. 3, pp. 420, 521, 522, 523; Rodemyre, History of Centralia, p. 59; Dyer, Autobiography and Reminiscences, pp. 111, 112; Gentry, Some incidents of the Civil War in Boone County, p. 17 1/4; History of Boone County, p. 462; St. Louis Daily Union 29 Sept. 1864, p. 1