General Clarence Potter had sent a memo to Generals Cummins and Forrest outlining his concerns that the U.S. had established agents in the same way that the Confederates had in the U.S. War Department. Forrest met with Potter to discuss his concerns and ordered him to try to devise a way to catch such agents.
While Potter was busy with his own duties, the problem ate at him until he came up with an idea. He routinely sent multiple copies of reports to various departments within the War Department. He personally typed out one such report with different phrasing in each copy and sent them out as usual. Eventually, he received a copy of the key phrase back from one of his own agents in the U.S. War Department. The particular report had gone to the Operations and Training Section within the War Department which narrowed down where the particular gopher was located.
After reporting this to Forrest, Potter was ordered to send a second set of reports to O and T's various sub-sections each again having a different wording of key phrases. Forrest also ordered Cummins to investigate the Section using more conventional methods. This second go-round succeeded and a clerk named Samuel Beauchamp Smith was arrested and interrogated.
"Gopher" is likely a twee variation on the word "mole". Aside from the punning, this difference is a way of illustrating the story is set in an ATL.