The short answer is that the 12th and 13th stars represent,
respectively, Missouri and Kentucky.
As you may have read, both Kentucky and Missouri proclaimed neutrality early
in the war. In the case of Missouri, that neutrality was broken when US
forces under General Nathaniel Lyons arrested the Missouri State Guard at
their summer encampment, and imprisoned them in St. Louis. His forces then
proceeded up the Missouri river to Jefferson City, forcing the State
government into exile. This began a civil war between the Missouri State
Guard and the United States forces. The Missouri government retreated to the
town of Neosho in the southwestern corner of the state. The legislature went
into a special session, and on 31 October 1861 adopted an Ordinance of
Secession. On 28 November 1861 the Confederate Congress passed an Act
admitting Missouri as the 12th state of the Confederacy.
The Union response in Missouri was to organize a state convention, which
declared the state government to be deposed, and organized a provisional
state government. As a result, Missouri had two state governments: the
elected government which seceded and joined the Confederate States, and the
provisional government created by Unionists to remain with the United
States.
In Kentucky, the actions were essentially a mirror image of Missouri.
Kentucky's neutrality was broken when CS Gen. Leonidas Polk moved his troops
to Columbus, Kentucky, one day before US General Ulysses Grant moved his
army into Paducah, Kentucky. The legislature of Kentucky had been elected on
a pledge of neutrality backed by a secondary pledge to go with the South if
neutrality proved impossible. However, when the neutrality was broken, the
legislature cast its lot with the North, on the grounds that the Confederacy
had been the first to break the neutrality. Southern sympathisers in
Kentucky were furious. They replied that Polk's move had been necessitated
by Grant's preparations, and that the pro-Union members of the legislature
had broken their campaign pledge.
As a result, a convention with delegates from most of Kentucky's counties
met at the town of Russellville and adopted a Declaration of Independence.
In the same fashion as the pro-Union convention in Missouri, the
pro-Confederate convention in Kentucky deposed the elected state government
and created a provisional government loyal to the Confederate States. By an
Act of Congress approved on 10 December 1861, Kentucky became the 13th state
admitted to the Confederacy.
So Missouri and Kentucky had representatives in both Congresses and
regiments in both armies. They were not alone in this. Virginia and
Tennessee also had Unionist congressmen and army regiments, and there was
even a provisional government of Virginia which was recognized by the United
States. The only reason I can think of that Missouri and Kentucky are
treated differently in most history books from the rest of the Confederate
States is that their secessions took place well after the outbreak of
hostilities, and as a result large portions of their territory were pretty
quickly overrun by US forces. Missouri was tenacious however. Her forces
kept returning, and as a result the number of battles fought in Missouri
were only surpassed by the number in Virginia and Tennessee, respectively.
Devereaux D. Cannon, Jr.
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