The ninth season of the American science fiction television series The X-Files commenced airing in the United States on November 11, 2001, concluded on May 19, 2002, and consists of twenty episodes.

As such, the main story arc for the season follows Dana Scully (Gillian Anderson), John Doggett (Robert Patrick), and Monica Reyes (Annabeth Gish) on their hunt to reveal a government conspiracy involving the elaborate and malevolent creation of "Super Soldiers".

Season nine received mixed reviews from critics and garnered a negative reaction from many long-time fans and viewers, partially due to Duchovny's absence.

Critics blamed it on what they considered an increasingly incoherent story arc, while the cast and crew ascribed the drop in viewership to the September 11 attacks.

The show was unsuccessful and was canceled before any story arcs were resolved, but The X-Files episode "Jump the Shark" was written to give closure to the series.

Doggett asks Scully for help on a case involving an EPA official, Carl Wormus (Nicholas Walker), who died after his car was forced off a bridge by a woman he picked up.

Doggett and Walter Skinner (Mitch Pileggi) travel to a reclamation plant, looking for links between Wormus' work and death.

After doing an illegal autopsy on Wormus, Alvin Kersh (James Pickens, Jr.) sends Brad Follmer (Cary Elwes) to locate Doggett.

The investigation at the reclamation plant leads to an unknown woman, whose identity is later revealed to be Shannon McMahon (Lucy Lawless), one of Doggett's former Marine associates.

Misled by the FBI, the agents enlist the help of The Lone Gunmen to protect Scully's son after they learn that the cult intends to kill the child.

With the help of Kersh, Scully, Reyes, Doggett, Spender, Marita Covarrubias (Laurie Holden) and Gibson Praise (Jeff Gulka), Mulder breaks out, and Mulder and Scully travel to New Mexico to find an old "wise man", later revealed to be the "Cigarette Smoking Man" (William B. Davis).

Cigarette Smoking Man appears to be killed by a missile, launched under the command of Knowle Rohrer (Adam Baldwin), who is revealed to be alive and well.

Eventually, however, several crew members began to develop new script ideas for the ninth season, many of which excited Carter.

[15] In addition, Elwes was cast to portray the new recurring character, Brad Follmer, an Assistant Director at the FBI, and Alan Dale was also written into the show as a new "villain", the "Toothpick Man".

Lucy Lawless was cast as the intended-recurring character Shannon McMahon, but she became pregnant after filming the season premiere, and—due to her high-risk pregnancy—had to leave the series.

[21] Realizing his importance in the series, Chris Carter and his crew opened negotiations with Duchovny in the hopes that he would reprise his character for the finale.

A former writer for The Lone Gunmen Thomas Schnauz joined the writing staff as a story editor and wrote two episodes.

Co-executive producer Michelle MacLaren and series writer John Shiban each made their directorial debuts, directing one episode.

[43] On May 19, 2002, the series finale, "The Truth", aired, and the Fox Broadcasting Company confirmed that The X-Files was not being renewed for a tenth season.

[43] Sabadino Parker from PopMatters, when commenting on the series finale, said, "It's also for the good, because The X-Files has long been but a pale reflection of the show it once was.

"[47] Brian Linder from IGN was more positive to the ninth season, saying that the series could still have aired if the writers created a new storyline for Robert Patrick and Annabeth Gish's character, which The X-Files crew did not do and continued what was seen by many critics as tiresome.

"[49] Entertainment Weekly reviewer Ken Tucker said the show operated in what he called "quaint territory", speculating that Chris Carter was the only one who seemed to understand the complex mytharc.

[50] Elizabeth Weinbloom from The New York Times concluded with, "shoddy writing notwithstanding, it was this halfhearted culmination of what was once a beautifully complicated friendship", between Mulder and Scully, ended remaining interest in what was a "waning phenomenon".

However he argued that the season contains a few "hidden gems" and praised those episodes which dealt with new material, while criticising other entries for focusing too heavily on "plotlines and characters from years gone by".