Murphy returned to Madison County following the secession vote. This account of what happened next is from Loyalty on the Frontier, written by Col. Albert Webb Bishop, who served with Murphy on the staff of the Union Gen. Samuel Curtis:
"Mr. Murphy was now permitted for a time to live in peace. At length, private threats were made; not to him directly, but in such a manner that they reached his family. Assassination was hinted at; and now, acting on the advice of genuine friendship, he secretly left his home, accompanied by Dr. J. M. Johnson and Frank Johnson, his brother, both citizens of Huntsville. They were followed, but evading pursuit, overtook the rear of General Curtis's army near Keitsville, Missouri. This was in April of 1862."
In his biography of Murphy, John I. Smith quotes Dr. Johnson's grandson who says that Dr. Johnson was warned by a woman that there was a plot to kill him, and that the doctor persuaded his brother and Murphy to flee.
Murphy joined Curtis's army only a month after the Battle of Pea Ridge. He apparently served on Curtis's staff while it was at Batesville, then served on the staff of General Francis Herron during the Battle of Prairie Grove. Meanwhile Murphy's daughters who had remained behind at Huntsville were looted of all their possessions by Confederate irregulars. This included Mary Murphy Lowe, the widow of a Confederate captain, who had come to live with Murphy after her husband was killed at the Battle of Wilson's Creek. When Gen. Herron learned of the plight of the Murphy women, he sent a detachment of troops to evacuate them to be with their father at Springfield, Missouri. Two of the daughters and a grandson would die shortly thereafter - Louisa, aged 24, on March 1, 1863; Laura, aged 22, on the 13th; and young Willie Lowe, aged 4, also on the 13th - reportedly due to exposure during their flight from Arkansas.
Next: Isaac Murphy Becomes Governor
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