When the Confederacy began to take shape in 1861, President Davis viewed the leaders of neutral Missouri with suspicion and initially refused to send military aid, so enabling the Union to dominate the state.

Upon Governor Jackson’s death from cancer on December 6, 1862, Reynolds started planning the liberation of Missouri with Confederate Major-General Sterling Price.

This duel never happened, however, as Brown chose "the common American Rifle with open sights, round ball not over one ounce, at eighty yards."

The public attacks continued and Brown, chafing under Reynolds' accusations of cowardice for his manipulation to avoid the original duel, finally issued a challenge.

The team, aware of the strong free soil sentiments of important factions of the Missouri electorate, had run as Douglas Democrats.

[4] At the beginning of the American Civil War, Missouri adopted a position that it would remain in the Union, but would not send troops or supplies to either side.

On May 20 Price dispatched Reynolds to Richmond in order to secure a guarantee from Davis to protect the state secession convention if reconvened.

Lyon demanded that the state government cooperate in suppressing the Southern rebellion, and that it permit federal military activities beyond the city limits of St.

Davis had his own concerns about the loyalty of Price and Jackson after the truce with Harney and their apparent willingness, based on the June 12 proclamation to resist the Confederacy.

Governor Jackson in his proclamation makes a merit of having proposed them; now if I agree to send Confederate troops into Missouri at your request, can you give me any guarantee that Mr. Lincoln may not propose and Governor Jackson assent to the agreement rejected by General Lyon, and compel those troops to retire before their joint forces?Davis did, however, authorize Benjamin McCulloch to provide any necessary military assistance to Missouri consistent with protecting Arkansas and the Indian Territory.

Davis was also unwilling to place in command of the area any general from the states of Missouri, Texas, or Arkansas—fearing that their objectivity for the entire Confederate war effort would be blinded by local concerns.

Meeting with Davis and secretary of War James Seddon, the Missourians received the immediate assignment of Price west of the Mississippi with his troops to follow when circumstances warranted.

"[10] Reynolds tried to exert his influence, backed up by his personal relationship with Jefferson Davis, over the civil and military decisions in the Trans-Mississippi Department.

He brought some order to the records of the government which he had inherited from Governor Jackson but early on had differences with Price over the disbursement of the dwindling state treasury.

The split became open and public when Reynolds appointed Colonel L. M. Lewis to the Confederate Senate to replace Price favorite and Davis critic, incumbent John B.

Reynolds' final chance to become governor in fact occurred in October 1864 when he accompanied General Price in his raid back into Missouri.

[12]Reynolds was proud of his own participation in the raid, claiming he had "been among the bullets on the battlefield, shared mule meat with the starving, and walked in the retreat".

"[14] Reynolds and a group of refugees including Kirby Smith, Sterling Price, John B. Magruder, and Joseph Shelby, with several hundred of his troops, retreated to Mexico in the summer of 1865.