FBI Deputy Director Alvin D. Kersh was a Navy A-6 Intruder weapons officer during the Vietnam War. He is known for using the same instincts that served him as an aviator in the military to guide his career in the FBI.

As an Assistant Director, he temporarily became supervisor to Agents Fox Mulder and Dana Scully when they were assigned away from the X-Files division. During this time, the Cigarette Smoking Man could be seen in his office, reminiscent of his silent presence in Walter Skinner's office in earlier seasons. Kersh assigned Mulder and Scully mostly to menial tasks, such as terrorist details and Federal background checks. When they did investigate an X-File behind his back, Kersh would charge them for expenses they incurred on the case, forcing them to pay out of their own pocket. He also attempted to separate Mulder and Scully, believing that Mulder threw away a promising career as a criminal profiler, but that Scully's career could still be saved.

When Mulder and Scully were reassigned to the X-Files Section, Kersh continued to climb the ladder, culminating in an assignment as Deputy Director. It was not long after his promotion that Mulder was abducted by aliens. Kersh assigned John Doggett to run the manhunt for Mulder. When Mulder returned, Kersh refused to assign him to the X-Files, keeping Doggett in that position. When Mulder and Doggett pursued an unauthorized case, Kersh was prepared to fire them both, but Mulder accepted full responsibility and was dismissed from the FBI. Shortly thereafter, Mulder disappeared again, and Doggett brought in Monica Reyes to assist him investigate Kersh's involvement in the conspiracy surrounding Mulder's disappearance. The investigation turned up nothing. Although Doggett seemed convinced that Kersh was involved in the conspiracy, Kersh insisted that he was actually protecting Mulder.

During the ninth season, the Toothpick Man, a key conspirator, could be seen in the company of Kersh, much like Cigarette Smoking Man before. In the end, Kersh showed a heroic side when during the series finale, he assisted Doggett and Skinner free Mulder from a military prison. Following this, Kersh had to permanently close the X-Files to appease his irate superiors. The X-Files are still officially closed when Mulder consults with the FBI 6 years later when FBI Agent Monica Bannon goes missing, however, Kersh is noticeably absent.