In 2375, Dougherty entered into an alliance with the Son'a, led by Ahdar Ru'afo, to covertly relocate the Ba'ku from their home in an area of space known as "the Briar Patch," and then perform a procedure to collect metaphasic particles from the planet's rings. As this procedure would leave the planet uninhabitable, Dougherty and Ru'afo were forced to develop a plan whereby the Ba'ku would be transported to another planet using a holoship, leaving the Ba'ku completely unaware of what was transpiring. This would leave Dougherty and Ru'afo free to collect the particles, which had rejuvenating qualities, without killing the inhabitants. Although Dougherty had secured permission from the Federation Council to execute this mission, he actively attempted to prevent the details of the operation from reaching them, knowing that, if it were to be learned that the Federation had sanctioned the forced relocation of a peaceful people, public opinion would turn against him, and he would be unable to proceed.
Dougherty's plans were complicated, however, when the crew of the USS Enterprise uncovered the plot. As Captain Picard and members of his crew acted to protect the Ba'ku, Commander Riker, the Enterprise's first officer, attempted to reach the perimeter of the Briar Patch in order to contact the Council and inform them of the details of Dougherty's operation. Dougherty was initially reluctant, but Ru'afo convinced him to let two Son'a battle cruisers intercept the Enterprise, explaining that, if the Federation were to learn the truth, the operation would be halted, and the Federation would lose an invaluable opportunity. Later, upon learning that the Son'a and the Ba'ku were, in actuality, the same race, and that the Son'a were simply attempting to gain revenge on those that had exiled them, Dougherty ordered Ru'afo to halt the operation. However, Ru'afo responded by viciously beating Dougherty and restraining him in a device designed to stretch the flesh of one's face tighter. Dougherty then warned that if the operation went ahead, the Federation would pursue the Son'a. Ru'afo responded that the Federation would never know what had transpired, before activating the device, killing Dougherty. (Star Trek: Insurrection)
Matthew Dougherty was played by Anthony Zerbe.
Developing the character
The first material evidence of Dougherty's existence was in a story treatment for the ninth Star Trek film (which became Star Trek: Insurrection), dated 23 June 1997. In that treatment, he was characterized as a Federation ambassador who was aged thirty-eight and had the first name "Matt". He was initially described in the same document as "the Federation's Romulan envoy". As was revealed during the course of the story, he had negotiated an agreement with the Romulans to move a group of aliens off a particular planet, in order to make sarium krellide beneath the planet's surface available to the Federation and the Romulans. When Picard discovered the truth and began to rebel against the ambassador, Dougherty ordered Riker to arrest Picard. However, it was ultimately made clear to Dougherty, when hundreds of Federation colonists arrived to join the rebellion, that he had lost. Regarding the final encounter between him and Picard, the document stated, "Ever the diplomat, Dougherty tries to put a spin on the events that makes everything okay." He took some credit for the Federation Council having decided there would be no formal charges against Picard. Dougherty even now respected Picard for the stand he took but the ambassador tried to dissuade him from taking the matter further, on Earth, though Picard implied he was indeed about to diplomatically oppose Dougherty further. (Fade In: The Making of Star Trek Insurrection)
In a story outline dated 25 July 1997, Ambassador Dougherty's part in the story was replaced by an unnamed "senior admiral" at Starfleet. When Picard proved reluctant to move the aliens (who were by now named the Ba'ku) against their will, the admiral ordered the Enterprise to leave their star system, allowing other Starfleet ships to do the job instead. As before, the admiral eventually responded to Picard's rebellion by ordering Riker to arrest Picard, though Riker ultimately didn't do so. This was the last mention of the admiral in that document. (Fade In: The Making of Star Trek Insurrection)
After Michael Piller wrote a first draft script for the film, Admiral Dougherty was mentioned in a memo Piller wrote to Rick Berman on 22 September 1997. In that message, Piller observed that Dougherty himself had been sent to terminate Data, as the android had gone "berserk". The memo also regarded Dougherty as a sinister influence within the Federation. (Fade In: The Making of Star Trek Insurrection)
Piller wrote more about Admiral Dougherty in a second draft script for the film. "I'd moved the admiral in charge of the nefarious mission to be aboard the Son'a ship," remembered Piller. "That would give me the power of the Federation right there to confront Picard, eye to eye [....] [Compared to the villainy of Ru'afo,] the moral ambiguity of Admiral Dougherty was more interesting to me. He was a decent man who thought he represented a noble cause and during the film, slowly compromises his ideals to get the job done. The trick would be for the actor cast to play his part as though he were the hero of the piece. In fact, I thought Dougherty was the true villain of the movie and the character who might prove to be the most memorable antagonist to Picard." In the same draft of the script, Dougherty was killed by Ru'afo. Despite being the second draft Piller had written for the movie, this script – dated 15 November 1997 – was the first one he submitted to Paramount Pictures. About a week thereafter (on 3 December 1997), the studio executives at Paramount wrote a memo to the "Star Trek team" which suggested Dougherty might "share more of a backstory" with Picard and that, since it seemed unclear whether the admiral or Ru'afo was the main villain until after Dougherty's death, power might be unequivocally seized away from him by Ru'afo earlier in the story, specifically after Picard refused to follow the admiral's commands. The memo proposed that Dougherty could perhaps object to Ru'afo taking control but that the admiral's threats might "ring hollow", because he was already so entrenched in the conspiracy. (Fade In: The Making of Star Trek Insurrection)
In a character description that was written by Michael Piller and was used by Casting Directors Junie Lowry-Johnson and Ron Surma to seek a performer to play the role, Dougherty was described thus; "Human male Starfleet Admiral in his 60’s. He has been assigned to help Ru’afo and the Son’a for what seem to be the most noble of reasons, or at least he has convinced himself that the reasons are noble. But as Picard begins to interfere with their plans, he begins to make moral compromises that lead him into making tragic errors." (Fade In: The Making of Star Trek Insurrection)
Dougherty's first name of "Matthew" comes from the revised final draft script of Star Trek: Insurrection. That screenplay also referred to him as being sixty-nine years old as of the film's setting in 2375, suggesting he was born in 2306. The script further described him as "a confident, charismatic officer." 
Anthony Zerbe was cast as Admiral Dougherty after auditioning for the role of Ru'afo. "He did a fascinating reading," Director Jonathan Frakes reflected, "and even threw in some classic poetry, something from Dante as I recall." When F. Murray Abraham received the part of Ru'afo, the casting team immediately selected Zerbe to portray Dougherty. (The Secrets of Star Trek: Insurrection, p. 122)
At first, the fact Anthony Zerbe was almost entirely unfamiliar with Star Trek influenced his performance as Dougherty. "As a matter of fact, one of my first lines was about Commander Data [pronounced Day-ta], and so when we had the [table] reading, I said, 'Commander Data [as in Dat-a]. We can't find Commander Dat-a.' Thirty heads turned to me in unison and said to me 'Day-ta.' I was chagrined. I learned how to pronounce it quickly." (Cinefantastique, Vol. 30, No. 12, p. 28) This initial experience of Zerbe portraying Dougherty was followed by Rick Berman approaching the actor after the table reading and arranging to send Zerbe "a couple of shows." (Star Trek: Insurrection - Official Movie Souvenir Magazine, p. 35) The actor continued, "They sent me the two prior films, and I studied the script. The guys that wrote it made themselves available to me, just to come into whatever it is, the 25th [sic] century." (Cinefantastique, Vol. 30, No. 12, p. 28) Zerbe found that watching the pair of movies helped him prepare for the role. (Star Trek: Insurrection - Official Movie Souvenir Magazine, p. 35)
Anthony Zerbe thought deeply about his part as Admiral Dougherty. "I play [Picard's] boss. He's a little political, he's very high-up," the actor remarked. "Whereas [...] Picard is the maverick, you know, he's kind of like the Rommel. I think of him as Rommel, and [Picard] would be my lead-tank guy [....] But I finally have to keep my eye on him." ("Making Star Trek: Insurrection", Star Trek: Insurrection (Special Edition) DVD/Blu-ray special features) Zerbe additionally commented, "Dougherty is a politician, and politicians [even military ones] tend to feel that the end justifies the means, so he has to take that position here. There are six hundred people on the planet, and if we have to lose 600 to help billions, that's okay with him. But it's not okay with Picard." (The Secrets of Star Trek: Insurrection, p. 25) Zerbe even admired the character, saying, "I like Admiral Dougherty. I think that, even though it is not fashionable for the end to justify the means, it certainly is the way life works sometimes, thankfully." (Cinefantastique, Vol. 30, No. 12, p. 28) Zerbe especially liked that the character figures prominently in the storyline of Star Trek: Insurrection. "Dougherty makes a lot of sense to me," he admitted. "He's thinking in the largest sense of where this metaphasic radiation [that surrounds the planet Ba'ku can go], how it can be used to create new medicines and to help millions of people. He has to ask himself, 'Do we really need to worry about 600 people on the Ba'ku planet when you think about where this can go and what can happen?' So, that's a global thinking as opposed to Picard's more personal thinking. So in that way, I can certainly defend Dougherty quickly and easily." (Star Trek: Insurrection - Official Movie Souvenir Magazine, p. 35) Chuckling, Zerbe added about Dougherty's dilemmas, "Fortunately for me, I never really have to deal with those things. That's why I like this sort of vague reality I live in." Indeed, Zerbe thoroughly enjoyed playing Dougherty. (Cinefantastique, Vol. 30, No. 12, pp. 28 & 29)
Anthony Zerbe regarded the way in which Dougherty is killed as being similar to another death scene he himself performed, as Milton Krest in the James Bond film License to Kill. Once he was shown where Dougherty's death scene was to take place, Zerbe had to perform it, as the admiral's death was planned to be achieved using a combination of CGI and live-action footage of the actor. "They wanted me to scream all through that, which I did," he recalled. "They took a lot of still photographs." (Cinefantastique, Vol. 30, No. 12, p. 29) Portraying Dougherty's death additionally married prosthetics, cyberscanning and morphing, with 3D ripple effects and shadows added by Blue Sky/VIFX to enhance the footage. Initially, Michael Westmore's makeup effects team built, as a starting point, a twisted face, using hand-laid strands of hair to represent Zerbe's white beard. Viewpoint DataLabs International, Inc., hired to execute cyberscans of the actor in various facial positions, then used in-house software that enabled them to create five NURBS surfaces – head, eyelids and ears – from the 350,000 points of data gathered during a face scan in which Zerbe's expression had been neutral. Morph target points were then created for Softimage animation. In order to film the end of the shot, the set had been rebuilt on stage at Blue Sky/VIFX. "In the main unit coverage, there was no B-side of the prosthetic for after-death shots," explained BS/VIFX Visual Effects Producer John Kilkenny. "We shot the B-side here [during post-production], matching it to first unit's stuff, while adding dripping blood, scars and stretching skin." This filming involved Zerbe, Kilkenny and BS/VIFX Effects Supervisor Jim Rygiel. Once all the necessary footage had been shot, the Blue Sky/VIFX team produced morphs between the facial scans and the earlier-created Westmore makeup, creating the semblance of tearing skin and crushing bones. "The scan data let us morph between the A-plate to the B-plate to complete the illusion of this killer facelift," Kilkenny concluded. (Cinefex, No. 77, pp. 88 & 87)
Playing Dougherty required that Anthony Zerbe return to do some dubbing. That experience allowed him to view some footage of the movie. (Cinefantastique, Vol. 30, No. 12, p. 29)
Dougherty made an impact on Picard actor Patrick Stewart. "Anthony Zerbe's role is the most complex one in the movie," Stewart reckoned. "He's the one who has to deal with his loyalty to the Federation while at the same time accommodating the evil wishes of the Son'a. He's a man who we see is torn by his professional dilemmas. And of course, before the end of the movie, we see him literally torn by something physical as well!" (The Secrets of Star Trek: Insurrection, p. 123)
Jonathan Frakes once described Anthony Zerbe's portrayal of Dougherty in Star Trek: Insurrection as "great". (audio commentary, Star Trek: Insurrection 2010 DVD/Blu-ray) On another occasion, Frakes enthused, "Zerbe is, in many ways, a more conniving villain than [Ru'afo]." (Cinefantastique, Vol. 30, No. 12, p. 33) He also approved of the face-stretching effect that results in Dougherty's death, about which Marina Sirtis agreed, "That's a brilliant effect." (audio commentary, Star Trek: Insurrection 2010 DVD/Blu-ray) Zerbe's portrayal of Dougherty also impressed Rick Berman. (Star Trek: Insurrection - Official Movie Souvenir Magazine, p. 12)
In the novelization of Star Trek: Insurrection, Dougherty was established as being married to Madalyn, a woman thirty years older than him. He remained happily married to her until 2374, when she passed away.
According to the Star Trek: Section 31 novel Rogue, Dougherty was a member of Section 31. In Abyss, Elias Vaughn described Dougherty as "a single rogue admiral, now dead, who was working with the Son'a".