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During the seventh season, Mulder eventually discovers the truth about his sister.
Samantha was abducted (either by the alien colonists or the government conspirators), and various tests were performed on her.
His quest and belief in the existence of aliens was, for most of the series, the driving force of the plot, or mytharc.
However, during a period of time after Scully's cancer went into remission (season 5), Mulder was convinced by Michael Kritschgau that aliens did not in fact exist, and that the government conspirators had merely concocted that threat as a smokescreen, to justify military activities and toy with him.
"If there was a profiler like himself profiling him he would have to work from the fact that he has some oral fixation because he is constantly popping sunflower seeds.
He doesn't have a bedroom, you've never seen him in his bed, you've seen him sleeping only in the couch." Despite his aloofness and cynical sense of humor, Mulder displays unbridled enthusiasm and interest when it comes to the paranormal, especially because of his personal involvement after his sister's abduction.
In a vision of Scully's, Mulder falls sick to the disease, but refuses the Smoking Man's help and his proposal to join his elite.
Mulder is saved by Agent Miller and they regroup with Scully, however, she says Mulder needs a blood transfusion and only their son can give it to them.
She was unable to bear the testing any longer so she ran away from her home and was eventually admitted to a nearby hospital, where she disappeared from her locked room.
Scully mentions that he is wanted by the FBI and dialogue also shows that the FBI does not really want to find him and is simply happy to have him "out of their hair".
He is called to assist with the investigation of a missing FBI agent.
Mulder was a main character for the first seven seasons, but was limited to a recurring character for the following two seasons.
He returns as a main character for the tenth and eleventh seasons.
At that moment, an unidentified flying object hovers over the trio, which is where season ten ends.