It was the largest find in Civil War history in a generation: Hours before he was gunned down at Ford's Theatre on April 14, 1865, President Abraham Lincoln pardoned a Union soldier court-martialed for desertion and saved him from execution.

The pardon, written in Lincoln's hand, was discovered 13 years ago by Thomas P. and Beverly Lowry, amateur historians from Prince William County who were poring over rarely touched files at the National Archives. Part of a treasure trove of courts-martial with Lincoln's signature and comments, it was a testament to the president's compassionate nature.

Thomas Lowry, 78, was catapulted to fame as a chronicler of Civil War military justice. The pardon, exhibited at the Archives' rotunda in downtown Washington, became a new thread in the narrative of one of history's most famous assassinations.

Except that it wasn't.

The Archives on Monday accused Lowry of altering the pardon in plain view in the agency's main research room to amplify its historical significance. Lincoln had indeed issued a pardon to Pvt. Patrick Murphy, but the 16th president did it exactly one year to the day before he was assassinated by John Wilkes Booth. Archives officials, after a year-long investigation, say Lowry signed a written confession Jan. 12 that he brought a fountain pen into the research room sometime in 1998 and wrote a 5 over the 4 in 1864, using a fade-proof ink.

Lowry, a retired psychiatrist who discovered the pardon in an unsorted file box, has denied any wrongdoing. He said he was pressured by federal agents to confess.

"I consider these records sacred," he said in an interview Monday at his Woodbridge home. "It is entirely out of character for me. I'm a man of honor."

His wife, Beverly, said the change was made by a former Archives staffer, a charge the agency denies.

There were no security cameras at the time to record what happened in the room. Lowry cannot be charged with a crime because the statute of limitations on tampering with government property is five years.

As the accusations flew over who altered the documents, Archives officials acknowledged that, in balancing security with providing open access to government records, they were too trusting. "It's horrible," the agency's head, David S. Ferriero, said in an interview. Ferriero, whose title is archivist of the United States, said the Lowrys became well known to the Archives staff and other researchers as, over a period of years, the couple indexed tens of thousands of courts-martial of Union soldiers. "This is a situation of having instilled a lot of trust in a regular user and not being suspicious," Ferriero said.

Lowry said that when he found the pardon, the "5" appeared to be a little darker than the other numbers in "1865." But he chalked it up to the fountain pen Lincoln used. "If we thought there was something funny about it, we would have called somebody," he said.

The inspector general for the Archives, Paul Brachfeld, said Lowry "willingly provided specific details" of how he altered the pardon, which reads: "This man is pardoned and hereby ordered to be discharged from the service." Signed "A. Lincoln," it is one of 570 documents with Lincoln's signature the couple discovered in the Archives.