The X-Files is one of the biggest and most influential sci-fi shows in TV history, but while Fox Mulder and Dana Scully have become as iconic as the show itself, they’re not the only important X-Files characters. Others, like Robert Patrick's John Doggett, have been introduced along the way and then later left the picture.
Part of what makes The X-Files such a success is not just the unbelievable cases that Mulder and Scully investigate, but that the pair’s contrasting sensibilities: Mulder's open-mindedness and Scully's skepticism create the perfect balance for the show’s supernatural content. Mulder is fundamental to The X-Files, but his character exits at the end of season 7, with his disappearance and abduction acting as a major narrative drive through seasons 8 and 9. The finale of the series’ original run of episodes revolves around Mulder’s return, and he later went on to reclaim his lead role in seasons 10 and 11 of The X-Files' limited revival.
During Mulder’s absence in season 8, John Doggett steps in as Mulder’s replacement and a new foil for Scully. Doggett eventually becomes even more important as both he and Monica Reyes (Annabeth Gish) become The X-Files’ new focus. Doggett even receives his own mystery and motivation that surrounds the death of his son, Luke, which mirrors Mulder’s own tortured backstory regarding his abducted sister, Samantha. Despite all of the work that’s put into John Doggett, the character disappeared from the series following season 9’s finale and was also absent from the subsequent X-Files feature film.
After the conclusion of The X-Files and the release of the first movie, fans were eager to see some sort of continuation, which eventually arrived in 2008’s The X-Files: I Want to Believe. The X-Files is a series with an incredibly dense lore, but the goal of this new film was to shed all of this extraneous baggage and create an accessible standalone story that didn’t require the audience to be hardcore fans in order to follow the story. As a result, I Want to Believe steps away from the complex alien invasion mythology and instead tells a smaller story about faith. At its core, the new film strives to be a meditation on Mulder and Scully’s relationship, with everything else stripped away. If topics like an impending alien invasion were deemed irrelevant for the movie, then extraneous characters like John Doggett were even more superfluous. Even larger topics like Mulder and Scully’s child are basically ignored.
It’s understandable that a movie that wants to dig deeper into Mulder and Scully’s relationship dynamics would remove any supporting characters that could pull away attention from their story. I Want to Believe introduces new X-Files agents, played by Amanda Peet and Xzibit, but they’re merely exposition devices and people for Mulder and Scully to bounce off of. The decision to bring back Doggett, but relegate him to such a thankless role, would have been even more disappointing for fans than him not appearing at all. At least this way viewers are able to assume that he’s reached a happy ending. The fact that he becomes essentially a fugitive at the end of The X-Files series also makes a casual appearance more difficult to justify.
The new FBI agents who appear in I Want to Believe don’t return in the revival series and are of little lasting significance, which speaks more to the standalone nature of the movie. It’s worth pointing out that there’s no bad blood between Chris Carter and Robert Patrick, or any resentment associated with the Doggett character. Doggett’s absence in I Want to Believe is just to simplify the story and not confuse the audience, but Carter did try and bring Doggett back into the X-Files’ 11th and (seemingly) final season to help provide some closure to his dedicated character. Doggett was supposed to briefly return in an early season 11 episode, but scheduling conflicts prevented the casting from happening, which leaves Doggett’s X-Files ending still up to the audience’s imagination.