Even as Mulder is deceived by Special Agent Diana Fowley (Mimi Rogers), Scully stays true to the investigation, and the two find Spender to be a surprise ally.

The episode was well received by critics, who applauded the way the Syndicate's story arc was wrapped up, although others felt the resolution was too simplistic.

For the first five seasons of the series, FBI federal agents Fox Mulder (David Duchovny) and Dana Scully (Gillian Anderson) have unravelled a conspiracy that involves the mysterious Syndicate, and their plans to aid in the alien colonization of Earth.

Meanwhile, Mulder learned that The Smoking Man's (William B. Davis) ex-wife, Cassandra Spender (Veronica Cartwright), had successfully become an alien-human hybrid—a signal to the aliens for them to begin colonizing the planet.

At Fort Marlene, Mulder runs into the sickly looking Marita Covarrubias (Laurie Holden), who tells him that she was subjected to experiments by the Syndicate to create a black oil vaccine and that the colonists will begin colonization if they learn of Cassandra's existence as an alien-human hybrid.

Spender goes to the Syndicate's headquarters, only to find Krycek, who tells him that the group's members—with the exception of The Smoking Man, who has gone to retrieve Cassandra—are preparing to give Cassandra to the aliens.

Spender arrives at Fort Marlene, where he runs into Marita; she tells him to go to El Rico Air Force Base to find his mother.

Krycek finds the dead surgeon and the fetus missing, and tells Spender that the rebels are now going to succeed in their goals to halt colonization.

The next day, Mulder, Scully, Walter Skinner (Mitch Pileggi) and Spender report to Assistant Director Alvin Kersh (James Pickens, Jr.) on the deaths of the Syndicate and Cassandra.

Spender tells Kersh that Mulder and Scully could have prevented their demise, and recommends that they be reassigned to the X-Files before abruptly leaving the room.

[3] "One Son" concluded not only the story that had begun in the preceding episode, "Two Fathers", but also a large portion of the series' mythology, much of which had been centered around the Syndicate.

[8] The producers felt this was necessary as the Syndicate's story arc was becoming a "narrative drag" on the series, and that many questions from the past five seasons were still unanswered.

[10] Carter also sought to rectify small issues that fans had with the 1998 feature film, The X-Files, explaining, "I think if there was any trouble with the movie, it was that we promised so much that we didn't deliver all of it.

[8] Episode co-writer Frank Spotnitz agreed, saying that when The X-Files film was being promoted with the tagline "The Truth is Revealed," he realized that many fans would be unhappy with the revelations.

[16] "One Son" would be the last episode of the series to feature Owens' character, Jeffrey Spender, until the ninth season entry "William".

Bill Roe, director of photography, and Rob Bowman were tasked with lighting the entire structure for the episode's teaser and climax, a job that Spotnitz later called "amazing".

She was tasked with creating the illusion of the lead surgeon's head being frozen in liquid nitrogen, as well as "de-aging" members of the Syndicate for the episode's flashback sequences.

Meghan Deans of Tor.com wrote that the Syndicate handing over their family and loved ones to save the world was evidence of this permeating theme.

[36] Neal Justin of the Star Tribune also wrote about the episode's emphasis on family, commenting that "it is interesting to note that the core of the story appears to be the relationship between parents and their children".

A.M. Jamison of the Dayton Daily News wrote that "'One Son' ends dramatically, drawing to a close one quest and opening a new set of challenges not only for Mulder but the Earth as well".

[45] Robert Shearman, in his book Wanting to Believe: A Critical Guide to The X-Files, Millennium & The Lone Gunmen, rated the episode three-and-a-half stars out of five.

The author enjoyed Davis' performance, noting that he gave the role "real power", and that he was "the emotional centre of the episode".

[46] While critical about the amount of attention Fowley's allegiance received, Shearman ultimately felt that the episode "reaches for both significance and closure, and mostly works".

[46] Deans wrote that "One Son," along with "Two Fathers," is elevated above a "mytharc infodump" because of "its use of family, a theme woven deep and clear throughout".

[36] She largely applauded the episode's exploration of the various characters, and its central motif, noting that "the conspiracy [the Syndicate] is no longer the threat now.

[36] Tom Kessenich, in his book Examination: An Unauthorized Look at Seasons 6–9 of the X-Files wrote positively of the episode, saying "The 'Two Fathers'/'One Son' was extremely powerful stuff.

[49] Vitaris criticized the death scene of the Syndicate, noting that it was "clumsily contrived, allowing [The Smoking Man] and Fowley to escape, but not because it makes sense, but because the show needs them to return at some point".

Joyce Millman from Salon magazine said the episode, along with "Two Fathers," was one "of the most coherent, [...] almost unbearably tense, hours in the series' run".