He commandeered and armed the civilian vessel Union at Marion, Indiana for defense against Morgan's Raiders in July 1863.

[3] He also was elected a First Class Companion of the Indiana Commandery of the Military Order of the Loyal Legion of the United States.

The incident concerned an attempted arms shipment by the rebel ship Itata from the U.S. to Chile.

He was accused by opponents of the administration of having gone beyond his public orders to become involved in intrigues with the combatants.

Theodore Roosevelt defends Brown from these charges in his book, Campaigns and Controversies.