The episode ended with the confirmation that Spender and Mulder are half-brothers due to the Cigarette-Smoking Man’s affair with Mulder’s mom, but Spender seemed doomed to remain disfigured forever.
Spender certainly looks different in the new video than he did when last seen in Season 9.
In fact, he was so unrecognizable that Scully was almost able to believe that he was actually Mulder due to his knowledge of the X-Files and the DNA that seemed to match Mulder’s.
After being shot in the head by his father (who also happens to be the Cigarette-Smoking Man), Spender was subjected to horrible experiments that left him burned and disfigured to the point that not even Scully or Skinner recognized him.
…
Declassified: The End Of The World | Season 11 | THE X-FILES