Joseph Manderely was a former Interpol agent who assisted Majestic-12 in their attempts to exterminate the Knights Templar and establish dominance over Europe. As a reward for his service, Manderely was put into position as the acting head of UNATCO, as an inside man who would continue to report to Majestic-12.
At the start of the game, Manderely is under considerable pressure from Walton Simons, the director of FEMA, who has repeatedly acknowledged his dissapointment at Paul Denton's performance for their mutual cause. For his own sake, Manderely repeatedly urges JC to follow procedure and respect his superiors, hoping that JC's performance would relieve Manderely's pressure.
When JC defects to the NSF along with his brother, Manderely is held entirely responsible for failing to keep his agents in line. When JC confronts Manderely as he escapes UNATCO headquarters, the player is given the choice whether or not to kill him. If the player chooses to let him live, Walton Simons has Manderely executed for his incompetence and frames JC in the media, ostracizing him from the general public.