That was a fascinating segment years ago on "Unsolved Mysteries". But anyway...
Stanton was behind the plot.
Booth had the password to cross a bridge (closed at sundown at that time) to leave DC.
Had Booth's instructions been followed, the VP and Sec State would have been murdered on the same night, putting Stanton in the White House.
Lincoln's sole bodyguard (provided by Stanton? I can't recall) left his post and went to the nearby tavern, where Booth was drinking. Booth got up and left after the bodyguard arrived.
The missing pages from Booth's diary reportedly emerged from an old box in the eaves of Stanton's old house, sometime in the 1980s.
Stanton knew who to look for and where to look, and most of the conspirators were quickly rounded up, given a military trial, and executed before they could talk.
Years later, Theodore Roosevelt arrived at the home of Lincoln's son for an evening bull (moose) session, and found him burning papers in the hearth. Lincoln told Roosevelt that they pertained to a member of his father's cabinet who had been behind the assassination. Roosevelt suggested that those could be of interest to historians. Lincoln didn't seem to be concerned.
:')
Stanton had a bad habit of making famous documents disappear. He was also the last known owner of the infamous Dahlgren Papers that were found of the body of a union soldier and reportedly detailed a plot to assassinate Jefferson Davis. The Dahlgren Papers' custody is well documented throughout the war and after it until they were shipped with confederate government records to Washington, D.C. Upon arrival in Washington Stanton immediately sent for them and took possession. They were never seen again.