Apart from an encounter of opposing forces near Osawatomie in which he and his band were engaged, Brown took no share in the open fighting between the organized companies of opposing forces, and his part in the irregular guerrilla warfare of the period is uncertain.

Towards the close of the war one of his sons was shot by a preacher who alleged that he had been robbed by the Browns.

After peace had been restored to Kansas by the vigorous action of Governor Geary, Brown left the scene and never again took an active part in the local affairs of the Territory.
John Brown's influence upon the course of affairs in Kansas, like William Lloyd Garrison's upon the general anti-slavery movement of the country, has been greatly misunderstood and exaggerated.

Brown's object and intention were fundamentally contradictory to those of the freestate settlers.

They strove to build a free commonwealth by legal and constitutional methods.