Anatomy of an Assassination, by John Cottrell (New York: Funk & Wagnalls, 1966) describes how Dr. Ray Neff, a health sciences professor at Indiana State University with a chemistry background, de-ciphered coded messages left by Colonel Lafayette Baker, Union spymaster. Therein were found these lines:
In new Rome there walked three men, a Judas, a Brutus and a spy.
Each planned that he should be the king when Abraham should die.
One trusted not the other but they went on for that day,
waiting for that final moment when, with pistol in his hand,
one of the sons of Brutus could sneak behind that cursed man
and put a bullet in his brain and lay his clumsey [sic] corpse away.
As the fallen man lay dying, Judas came and paid respects to one he hated,
and when at last he saw him die,
he said, “Now the ages have him and the nation now have I.”
But, alas, fate would have it Judas slowly fell from grace,
and with him went Brutus down to their proper place.
But lest one is left to wonder what happened to the spy,
I can safely tell you this, it was I. (Lafayette C. Baker)
Baker identifies himself as “the spy”. Judas would be Edwin Stanton, believed to have said “Now he belongs to the ages” at the time the assassinated Abraham Lincoln breathed his last. But who was Brutus? Judas (Edwin Stanton) “fell from grace” and “with him went Brutus down to their proper place.”
Colonel Lafayette Baker is said to have died on July 3, 1868. However in an article published in the Idaho State Journal (Pocatello, Idaho), on November 4, 1977 (relevant excerpt hopefully viewable above), Vaughan Shelton claimed that Colonel Baker faked his “death” in 1868 and assumed a new identity: R.D. Watson of Fulton County, Kentucky. 
Vaughan Shelton was (or is if he yet lives) knowledgeable about the Lincoln assassination, having written the book, Mask For Treason, published in 1965. Lafayette Baker, according to a sidebar article in the Idaho State Journal (op. cit.), was a thoroughly disreputable character who “spent most of his time spying on Washington officials for the purpose of blackmail.” Baker also allegedly “lined his pockets” with profits from contraband and “other thievery.” A clique in the Union War Department (later renamed “Defense” Department), headed by Edwin Stanton (a.k.a. Judas), wanted to “eliminate” Lincoln. Colonel Baker hoped to make a name for himself by quickly “solving” the case, a “masterpiece of detective work by Baker.” But Baker’s hope for acclaim due to his “brilliant” gumshoe efforts came to naught. Instead, Baker “was fired in disgrace by Stanton in early 1866.”
Colonel Lafayette Baker “died” (switched identities) on July 3, 1868. Edwin Stanton died on December 24, 1869. Thaddeus Stevens, said to have been the “grandfather” of the Lincoln assassination plot, died on August 11, 1868. These three are my tentative candidates for Brutus (Stevens), Judas (Stanton), and the spy (Baker). Thaddeus Stevens is a problematical candidate since he is not clearly identifiable in the decoded “Judas, Brutus and the Spy” message left by Baker and later found by Ray Neff. (For background on Thaddeus Stevens as “grandfather” of the Lincoln assassination, see Addenda to the Addenda, Ersjdamoo’s Blog, July 14, 2015.)
A Montreal bank credit originally belonging to John Wilkes Booth, the actual shooter of Lincoln, was claimed by “R.D. Watson” in a letter to the War Department in 1870. “R.D. Watson” had been Colonel Baker’s main alias back when he, as such, was “alive.” “R.D. Watson” claimed the bank credit belonged to his late father, “Daniel Watson.” And who was this “Daniel Watson”? Given that it had not been John Wilkes Booth who had been killed on April 26, 1865 at Richard H. Garrett’s farm, but instead a “James W. Boyd”, Confederate soldier, “Daniel Watson” may have been a pseudonym being used by Booth. It is known that Booth and his “usual suspects” gang had been in contact with Colonel Baker at least as of March 19, 1865. Hypothesized is that “R.D. Watson” (Baker) was seeking the funds owned by “Daniel Watson” (Booth), possibly to be conveyed by Baker to the still-alive Booth.
The waters are murky here, but what else would you expect, given that we are dealing with a world of Civil War espionage? Copies of the 1870 “R.D. Watson” letter, an 1865 letter to John Surratt signed with Colonel Lafayette Baker’s known alias of “R.D. Watson”, and of an authentic document written and signed by Colonel Baker, were sent to two handwriting analysts. Those handwriting analysts both “agreed without qualification (in writing) that all three documents were written by the same person – that Lafayette Baker and the ‘R.D. Watson’ of 1870 (two years after Baker’s ‘death’) were the same man. Further research in Fulton County records confirmed the identification beyond question.” 
(See also: Notorious Colonel Faked His Death?, Ersjdamoo’s Blog, March 4, 2013.)
——- Sources ——-
 “The Lincoln Conspiracy Movie Based on Forgeries, Says Historian”, by Vaughan Shelton. Idaho State Journal (Pocatello, Idaho), Nov. 4, 1977.