Dougherty was an ambitious Starfleet admiral in charge of the Federation's joint operation with the Son'a. The plan was to harvest the metaphasic radiation located in a region known as the Briar Patch. Since the process would render the region uninhabitable, the Ba'ku, a people who had set up a colony on a planet in the region, would need to be forcibly relocated. The plan was to beam them to a holoship projecting an image of their village so they were unaware they had been removed.
As cover for the scheme, Starfleet and the Son'a launched a joint cultural observation of the Ba'ku. However, Data discovered the truth and exposed the observation team, taking them prisoner. Dougherty reluctantly accepted the help of the Enterprise in apprehending Data. This resulted in Picard also learning the truth and confronting Dougherty, making it plain he disapproved of the destruction of the Ba'ku culture.
Picard took a group of his senior staff down to the surface to protect the Ba'ku, sending the Enterprise to argue their case to the Federation Council. Dougherty was reluctant to authorise the use of force but agreed to a plan to beam the Ba'ku aboard by individually tagging them. Suspecting Commander Riker would not obey an order to return, Son'a leader Ru'afo managed to get Dougherty's agreement to send ships to "escort" them. This resulted in a battle in which one Son'a ship was destroyed and another disabled.
After Picard had been captured with some of the Ba'ku, Dougherty confronted him and threatened him with a court martial. Picard suspected Dougherty would be more likely to face one, since he had tacitly agreed to the attack on the Enterprise. He also revealed what the Enterprise crew had learned: The Ba'ku and the Son'a were the same species, with the Son'a being a rogue offshoot exiled after a failed coup.
With this information, and with Ru'afo now planning to activate the collector and kill everyone still on the planet, Dougherty tried to halt the operation but Ru'afo beat him and attached him to a machine designed to stretch skin. Despite Dougherty warning that the Federation would hunt him down, Ru'afo activated the machine, killing him.
Gene Hackman and Wilford Brimley were asked to play Admiral Dougherty.
Anthony Zerbe originally auditioned for the role of Ru'afo, but the the production team decided instead to cast him as Dougherty instead.
Sir Patrick Stewart wanted his long life friend Brian Blessed to play Admiral Dougherty. Blessed did over eight hundred hours of astronaut training at Star City in Russia, and remains the number one civilian on the wait list for the International Space Station.
Dougherty's first name is not mentioned in the film but appears in the script.
The Star Trek Novelverse portrayed Dougherty as an agent of Section 31, although the film makes no reference to the organization.