<P> Reluctantly accepting Krycek's assistance, Mulder, Doggett and Skinner learn that an alien virus recently created in secret by members of the United States government has replaced several humans, including Billy Miles and several high - ranking FBI personnel, with so - called alien "Super Soldiers". Krycek claims that the soldiers are virtually unstoppable aliens who want to make sure that humans will not survive the colonization of Earth . They have learned that Scully's baby is a miraculously special child and are afraid that it may be more powerful than they are . When Miles arrives at the FBI Headquarters, Mulder, Doggett, Skinner and Krycek help Scully to escape along with Reyes, who drives her to a remote farm . Shortly after, Skinner kills Krycek, and Scully delivers an apparently normal baby while the alien "Super Soldiers" surround her . Without explanation, the aliens leave the area when Mulder arrives . While Doggett and Reyes report to the FBI Headquarters, Mulder takes Scully and their newborn son, William, back to her apartment . </P> <P> Mulder goes into hiding, Scully is reassigned to the FBI Academy, and Reyes becomes Doggett's new partner at the X-Files . Doggett, Scully, and Reyes discover a conspiracy to place Chloramine in the nation's water, causing mutations and creating "Super Soldiers ." This leads them to a clandestine laboratory where a secret experiment connected to Scully's child, William, is underway . The X-Files' investigation is hampered by Deputy Director Alvin Kersh (James Pickens, Jr .) and Assistant Director Brad Follmer (Cary Elwes). Scully is hopeful about reuniting with Mulder after a stranger, "Shadow Man" (Terry O'Quinn), offers to drive Mulder out of hiding . She accepts his offer, but she and Mulder are nearly killed: The man is a Super Soldier . Later on, Scully, Doggett and Reyes find evidence of a dangerous UFO cult that has found a spacecraft similar to the one Scully studied in Africa two years ago . The cult kidnaps William, but is destroyed when the baby's crying activates the ship and kills everyone while leaving William unharmed . </P> <P> Doggett finds a strange, disfigured man in the X-Files office . At first he believes the man is Mulder, but it is actually Jeffrey Spender, Mulder's half - brother . Spender sticks a needle into William . The other agents believe the injection to be a virus of some kind, but it is actually a cure for William's powers . Mulder comes out of hiding to look for classified information at an army base and, after allegedly killing a supposedly indestructible "Super Soldier" Knowle Rohrer (Adam Baldwin), he is placed on trial to defend the X-Files and himself . With the help of Kersh, Scully, Reyes, Doggett, Spender, and Gibson Praise (Jeff Gulka), Mulder escapes . Mulder and Scully then travel to New Mexico to find an old "wise man", later revealed to be The Smoking Man, who tells them that the aliens will arrive in 2012 . Doggett and Reyes are confronted by Knowle Rohrer, who is killed by magnetite (the only known vulnerability of the "Super Soldiers"). The four agents then escape from a pair of black helicopters that kill The Smoking Man with missile fire . Scully and Mulder are last seen together in a motel room, facing an uncertain future . </P> <P> Fourteen years since leaving the X-Files, Mulder and Scully are contacted by media host Tad O'Malley who has uncovered possible evidence of the alien abductions being fabricated by the government to cover up their experiments on humans, and Mulder has a theory that everything that he and Scully were led to believe on the X-Files was made up by a conspiracy of men . Mulder and Scully find themselves being enlisted back to the FBI and working on the now reopened X-Files unit, which brings the attention of the alive Cigarette Smoking Man . </P>

Watch the x files season 4 episode 21