Quantrell continued to direct the movements of the guerrilla bands, but he was rarely engaged in any of the battles; the active service he delegated to the most strategical and unmerciful members of his command. Bill Anderson, a human tiger in disposition, was placed in charge of the full force when it was decided to move upon Centralia, a small town in Boone county, on the Wabash, St. Louis & Pacific Railway. On the 27th of September, one week after the attack on Fayette, the guerrillas, numbering one hundred and fifty men, headed by Anderson and that most ominous of banners, the black flag, with skull and cross-bones, marched upon Centralia, which they took possession of without resistance. After pillaging the place the guerrillas took up their station at the depot and awaited the coming of the train. They had not long to wait, for soon the shrill whistle of the engine, as it came thundering through a cut, drawing five passenger coaches loaded with soldiers and citizen travelers, announced the coming of the prize. The moment the train stopped the dreadful black flag was flung out and with the exchange of a few shots the messengers of death boarded the cars. Everyone on the train was ordered out and made to form in line, after which the thirty-two soldiers were separated from the other passengers and all disarmed. Now the breathless suspense, the terrible forebodings and the anxiety as to the fate that would be meted out to them! Every soldier was shot as unmercifully as if they had been obnoxious beasts or poisonous snakes. The passengers were relieved of whatever valuables they possessed, after which they were permitted to proceed on their journey.

In the afternoon of the same day and before the guerrillas had departed from Centralia, a body of Iowa volunteers, one hundred strong, under the command of Major J. H. Johnson, rode into the town and in the space of a few hours the two forces met and engaged in a terrible conflict. Again Jesse James, who was the best pistol shot in the guerrilla service, made a furious dash at Major Johnson and planted a pistol ball almost in the center of the brave Major's forehead. The guerrillas now rushed upon the terrorized volunteers with such resistless impetuosity that they broke in confusion. The fight became a massacre, and but very few of the brave volunteers escaped to convey to anxious friends the dreadful fate that had befallen their comrades. One of the militiamen had a very remarkable escape. Being badly wounded, in the early part of the fight, he remained unconscious, with the blood streaming from a saber gash in his head, until the foe had departed. When the fight was over the guerrillas went among the wounded and shot them with their revolvers, determined that not a soldier should escape. This single exception to the consummation of guerrilla vengeance was supposed to be dead, and he therefore escaped the crowning feature of that day's massacre. When consciousness was regained he found himself alone, among the dead bodies of his comrades, and his shouts for help brought to his assistance the services of a kind old negro woman who took him to her house and obtained surgical aid, so that in two week's time he was able to return home.

The result of the fight at Centralia was not such as brought great encouragement to the guerrillas; the victory they gained was at the cost of nearly fifty of their number, whom it would be impossible to replace, because men of their bold, reckless and desperate character are rarely to be found. It was therefore determined to again divide up into squads and renew the warfare which they had waged so successfully in the previous year. But the guerrillas never fought again as they had at Fayette and Harrisonville; their courage to meet an armed force seemed to have vanished.