Pike responded to the charges in a vitriolic letter to Hindman. "You dare to pretend, sir, that I might be disloyal, or, even in thought, couple the word treason with my name!" He closed the letter: "Whether I am respectfully yours, you will be able to determine from the contents." He took the charges to the Confederate Congress in Richmond. Pike was eventually cleared, helped in part by his friendship with President Jefferson Davis. He remained bitter about the affair and later told his daughter he resigned because he was tired of working for men of inferior intelligence.
Pike returned to his home in Arkansas and resumed his writing (and his involvement with the Freemasons). He was recognized both as a novelist and a poet. One of his poems, "Reflections," shows his bitterness over the war and his resolution to leave it behind:
Out on this wretched party-war!
Where the best weapons, trick, chicane,
And perjury and cunning are,—
Its picked troops, scoundrelism's train—
Where baser men outweigh the best,
Lies always over truth prevail,
Wisdom by numbers is oppressed,
Knavery at Virtue dares to rail,
Slanders the brightest name assail;
Victory in such a war humbles the victor's crest.
Henceforth, myself I dedicate
To other service. Let me read
Thy pages, Nature — though so late
Thy voice of reprimand I heed.
From bud and leaf, from flower and bloom,
From every fair created thing,
Thy teachings will my soul illume,
So long in darkness slumbering;
That when to life's bright sunny Spring,
Autumn succeeds, it may not all my hopes entomb.