text: the x - files ( season 9 ) 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 . season nine takes place after fox mulder ( david duchovny ) goes into hiding , following the events of the eighth season finale , " existence " . as such , the main storyarc 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 who are creating " super soldiers " . for this season , former series ' leads duchovny and anderson scaled back their involvement with the show , with the former only starring in the two episodes that formed the season finale , " the truth " . doggett and reyes became the show 's central characters , and former recurring character walter skinner ( mitch pileggi ) became a main character . series creator chris carter had hopes that the show could continue on with new leads , and the opening credits were accordingly redesigned again . season nine received mixed reviews by critics and garnered negative reaction from many long - time fans and viewers , partially because duchovny did not make regular appearances on the show , after fulfilling his contract in the previous season . during this year , ratings for the season fell dramatically — which critics correlated with the season 's incoherent storylines but the cast and crew ascribed to the september 11 attacks — fox eventually decided to cancel the series . during the airing of season eight , carter and the x - files production team had created and aired a spinoff titled the lone gunmen . the show was unsuccessful and was cancelled before any story arcs were resolved , but the x - files episode " jump the shark " was written to give closure to the series . the x - files storyline was continued with the 2008 theatrical film the x files : i want to believe and later with a tenth season in 2016 . plot overview after the eighth season finale " existence " , fox mulder ( david duchovny ) goes into hiding . dana scully ( gillian anderson ) is again reassigned to the fbi academy , and monica reyes ( annabeth gish ) becomes john doggett 's ( robert patrick ) new fbi partner in the x - files office . 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 . she reveals to doggett that she is a " super soldier " . this leads them to a clandestine laboratory where a secret experiment is taking place on board on a naval ship . they later find connections between the experiments on the ship and scully 's child , william . after scully begins to miss mulder , a complete stranger — the " shadow man " ( terry o 'quinn ) — offers his service to drive mulder out of hiding . scully takes the offer , but unknowingly gets herself and mulder in even more danger . the " shadow man " , who is revealed to be a " super soldier " bent on killing scully and mulder . after a chase through a quarry , the " shadow man " is destroyed after being exposed to magnetite . later , scully , doggett and reyes find evidence of a dangerous ufo cult which has uncovered a second spacecraft similar to one scully studied in africa two years ago . 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 . the cult , however , is successful in kidnapping the child . concurrent with these events , doggett is run over by a car , which sends him to the hospital . as follmer and the " toothpick man " ( alan dale ) try to uncover the plans of the three agents , scully and reyes leave washington , d.c. to find scully 's son . doggett finds a strange disfigured man in the x - files office ; believing he is mulder , scully has his dna tested , and the results reveal him to have the same pattern as mulder . the disfigured man sticks a needle into william , which the other agents believe to be a virus of some kind , but it is later revealed to be a cure for william 's powers . the unnamed man is later revealed to be jeffrey spender ( chris owens ) , mulder 's half - brother . in the season finale , mulder returns from hiding in the attempts of finding classified information at an army base . he is caught , however , after allegedly killing an apparently indestructible " super soldier " , which causes him to be tried before a military tribunal . 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 ) . he tells the two that aliens will begin colonizing the planet on december 22 , 2012 . 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 . mulder and scully escape , but become fugitives on the run from the fbi . the final scene of the season features the two in a motel room facing an uncertain — but possibly hopeful — future . production development following the eighth season of the x - files , david duchovny announced that he would be completely leaving the show . as such , the future of the show was up in the air . before greenlighting a ninth season , neither the fox network nor any of the ten thirteen productions members knew if creator chris carter would return for another season . with this being said , he encouraged the other members of the crew to continue the series without him . eventually , however , several crew members began to develop new scripts ideas for the ninth season , many of which excited carter . this new - found enthusiasm eventually caused carter to sign a contract with fox for another year . likewise , anderson signed on at the last minute , with her contract extension only lasting until the end of 2002 ; she specifically stated that she would leave the show following the conclusion of the season . due to the changes in the cast , during the ninth seasons , doggett and reyes became the series ' new leads . executive producer frank spotnitz speculated that the show could extend into a tenth and possibly eleventh season , if the show was able to attract an audience . however , the show lost viewers and was eventually cancelled by fox . with the news of the impending end to the series , the crew members decided to wrap up long - running plots . " jump the shark " , the final episode to feature the lone gunmen , served as a de facto series finale for the cancelled x - files spin - off series the lone gunmen . executive producer and co - writer frank spotnitz had to fight to get the episode made ; the studio informed spotnitz that they did not want to bring the characters back in any capacity , as fox reportedly " hated [ the ] characters " . similarly , " release " was written to create closure to the story of the murder of doggett 's son . the show 's crew and actors had a range of opinions about the show 's finale , " the truth " . carter said of the finale , " it 's the end — you don 't get another chance . so you 'd better put everything you 've ever wanted to put in into the episode . there were things to distract from what was going on . the band was breaking up . " gish said , " it did feel like a big movie set . we were on location , there was an enormous budget , and everyone came back . " davis said , " it was great that they brought us all back in the finale , that they found a way to get us all in again . " pileggi said , " i can remember the last day on the set . we shot a scene with gillian and myself , and that was it . and then i had to say goodbye to another family , another crew . i almost up , and gillian was standing there looking at me saying ' okay , go ahead , big guy ; get through this . ' it was tough . " patrick said , " it was pretty euphoric , and sad , and all those emotions you can imagine . a chapter 's closing , and we 're all moving on to something new and exciting . and yet we were all going to miss each other . " kim manners called the final scene " truly one of the most emotional experiences i 've ever witnessed in my life . " former lead actor duchovny said , " in some ways , psychically i didn 't really leave . it was nice to be able to – i 'm just really happy that i was able to come back and finish it . " casting with " nothing important happened today " , the style of the opening credits were changed from the original credits , which , more or less , had been the same for the previous eight seasons . the credits included new graphics as well as new cards for gish and pileggi . 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 . after the departure of duchovny , the show garnered much criticism by fans and critics alike , with many saying that the bond between mulder and scully was what actually kept the show together for the first seven seasons of the show . 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 . initially , they were unsure if he would appear , but he eventually elected to return . spotnitz said , " my impression from talking to him was that he still cares about the show . he 's still invested in it and certainly cares about [ mulder ] . and i think he recognized that it was the best thing for the show and the audience [ for him ] to come back and give closure to nine years of the series . " not only did duchovny return for the finale , he also returned to write and direct the episode " william " ; he even had a small cameo in the episode , appearing as a reflection in scully 's eye . three episodes later , duchovny returned as an actor for the season finale , " the truth " . crew chris carter served as executive producer and showrunner for the season and wrote nine episodes , including the two - part season premiere and season finale , as well as important mytharc episodes . spotnitz continued as executive producer and wrote seven episodes , plus receiving story credit for an additional episode . vince gilligan continued as executive producer and wrote three episodes . john shiban was promoted to executive producer and wrote two episodes , plus receiving story credit for an additional episode . david amann was promoted to supervising producer and wrote two episodes . steven maeda was promoted to executive story editor and wrote two episodes . former writer for the lone gunmen thomas schnauz joined the writing staff as a story editor and wrote two episodes . duchovny received story credit for a single episode . manners continued as co - executive producer and directed the most of episodes of the season with eight , including the two - part season finale . tony wharmby directed three episodes . series creator chris carter directed two episodes . co - executive producer michelle maclaren and series writer john shiban each made their directorial debuts , directing one episode . series writers frank spotnitz and vince gilligan each directed an episode , after previously directing their first episodes the previous season . the remaining episodes were directed by dwight little , cliff bole , and cast member david duchovny . cast main cast gillian anderson as special agent dana scully ( 20 episodes ) robert patrick as special agent john doggett ( 20 episodes ) annabeth gish as special agent monica reyes ( 20 episodes ) mitch pileggi as assistant director walter skinner ( 11 episodes ) a david duchovny as fox mulder ( 2 episodes ) b a ^ pileggi is only credited for the episodes he appears in . b ^ although only appearing in the two - part season finale , duchovny is listed in the opening credits . he also has a small uncredited cameo in " william " , and appears in archive footage in " trust no 1 " and " jump the shark " . recurring cast also starring james pickens , jr. as alvin kersh ( 7 episodes ) nicholas lea as alex krycek ( 2 episodes ) william b. davis as cigarette smoking man ( 1 episode ) guest starring episodes episodes marked with a double dagger ( ) are episodes in the series ' alien mythology arc . reception ratings the first episode of the season , " nothing important happened today " , gathered 10 . 6 million viewers , whereas the second part gathered only 9 . 4 million viewers . 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 . when talking about the beginning of the ninth season , chris carter said , " we lost our audience on the first episode . it 's like the audience had gone away , and i didn 't know how to find them . i didn 't want to work to get them back because i believed what we are doing deserved to have them back . " " the truth " received the highest nielsen household rating and viewership numbers of the season . it earned a 7 . 5 rating and gathered 13 . 25 million viewers in the united states . the loss of viewers resulted in this season seeing a 30 percent ratings drop when compared to the eighth season . reviews 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 . " 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 . aaron kinney from salon magazine was more negative to the new season , even joking about the new female lead , calling her a " peppy new female presence . " 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 . elizabeth 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 " . another review from the new york times said of the show , " the most imaginative show on television has finally reached the limits of its imagination . " the a.v. club listed the ninth season and the 2008 film the x - files : i want to believe as the " bad apple " of the x - files , describing the ninth season as " clumsy mish - mash of stuff that had once worked and new serialized storylines about so - called ' super soldiers ' " . m.a. crang , in his book denying the truth : revisiting the x - files after 9 / 11 , noted that season nine " does not have a great reputation among viewers " . 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 " . dvd release