"You can kill a man but you can't kill what he stands for. Not unless you first break his spirit. That's a beautiful thing to see."
—The Cigarette Smoking Man, "The Beginning"
The FBI and their allies have faced many monsters, many just acting on basic instinct. However, there are some, whether supernatural or not, that are just pure evil.
Examples from Millennium, which is loosely part of the franchise, can be found here.
All spoilers are unmarked. You Have Been Warned!
- The Cigarette Smoking Man (CSM), real name Carl Gerhard Busch, is the Arch-Enemy of FBI Agents Fox Mulder and Dana Scully. Unlike the other, more well-intentioned members of the Government Conspiracy he is part of, the CSM is nothing but a cold-hearted manipulator selling out humanity for his own protection and empowerment. Directly behind the assassinations of John F. Kennedy and Martin Luther King Jr., the CSM happily takes on any task to violently dismantle any threat to his power-hungry organization. He allows Scully to be abducted and tortuously experimented on, resulting in her being afflicted with cancer and rendered infertile, putting hundreds of thousands through similar horrors. Revealed to be the father of Mulder, the CSM makes multiple attempts on the latter's life, including trying to burn him alive and later puts him through further horrific experiments, and transforms his ex-wife and son's mother into a monstrous alien-human hybrid. With every alleged moment of humanity or interest in redemption proven to be truly hollow and self-serving, the Cigarette Smoking Man shows, time and again, just how heartless a man can be, even in a world of extraterrestrial threats.
- "Fire": Cecil L'Ively is a deeply sadistic Serial Killer who has the power to ignite things using his mind. Using these powers, Cecil targets various wealthy women by sending them love letters and stalking them. He then burns them alive and targets the rest of their family. After failing to murder Sir Malcolm Marsden, Cecil follows him and his family to the States, posing as a caretaker named Bob who he actually murdered sometime before. Meanwhile, Cecil poisons and murders the family chauffeur with a flame accelerant before going to a crowded bar and burning the place to the ground while watching the fire with a smile on his face. Cecil then drives the Marsden family to a party in Boston, in which he sets ablaze the building's 14th floor to stage a rescue of the children as a publicity stunt. Later that evening, Cecil attempts to finally burn and kill the entire Marsden family and agents Mulder, Scully, and Greene, including locking the children in a separate room to burn to death.
- "Irresistible": Donald "Donnie" Pfaster is an intimidating necrophiliac Serial Killer who once worked at a funeral home, but was fired upon being discovered to have such a fetish, collecting the hair and fingers of his victims when he has killed them. When Agent Mulder and Scully investigate the murders, Donnie kidnaps Scully and prepares to torture her, barely failing to kill her because of being distracted, allowing her to escape, and getting him arrested. Returning, Pfaster is freed by the titular vigilante Orison, who frees the prisoners so that he could kill them, thinking of it as a true punishment. Donnie escapes Orison, immediately continues his killings, and once again kidnaps Scully, having become obsessed with her after she became his only victim who had escaped.
- "Die Hand Die Verletzt": Phyllis Paddock is a demon who poses as a substitute teacher after being accidentally summoned; the person who summoned her happened to be an innocent little boy, who she immediately kills upon seeing, tearing out his eyes and ripping his heart out. Having once been worshipped by a cult, said cult had stopped worshipping her for unknown reasons, and to this end, Phyllis kills the stepdaughter of the cult leader by forcing her to slit her wrists and then kills the leader by having a snake eating her, and then forces the other members to commit suicide.
- "Fresh Bones": Colonel Jacob Wharton owns a Haitian refugee camp, but instead of taking care of the immigrants, Jacob kills them for no reason at all but his own sick amusement. Some of Jacob's victims include a former prisoner who knew voodoo named Pierre Bauvais; multiple other innocent immigrants; and even a completely innocent child who did nothing to him. He also kills his own henchmen when they try stopping him from committing his heinous crimes, and he even frames the murders of his henchmen on Pierre Bauvais.
- "2Shy": Virgil Incanto is a freelance translator who feeds on women's body fat to survive. To do this, Incanto preys on them mentally and emotionally, developing relationships that last weeks and months so they get attached to him. Once they do, Incanto violently forces himself onto them and sucks their body fat against their will and kills anyone who finds out about him, such as Detective Cross, whose body he dumps in the bathtub, and the sweet landlady whom he coldly ignores even when she's been very nice to him. A sadistic, manipulative predator who killed 47 women in 5 states, Incanto takes pleasure in knowing that "The dead are no longer lonely" because he fed not only on their bodies, he fed on their minds.
- "Oubliette": Carl Wade is a photographer's assistant and psychotic pedophile who kidnaps young girls and holds them hostage in his basement. Carl is responsible for Lucy Householder's trauma as he kidnapped her at age 7 and held her for five years, causing her to panic from light because she's been in the dark for so long. Developing a sexual obsession with a teen named Amy Jacobs, Carl kidnaps her, shoves her in the trunk of his car, threatens a tow truck driver with a tire iron when he attempts to help Carl with his car, and takes pictures of Amy screaming and scared while she begs him to stop; when she attempts to escape, Carl punishes her by depriving her of water. When the FBI show up, Carl drags Amy out of the basement and attempts to drown her in the river.
- "Revelations": Simon Gates is a wealthy and well-respected businessman who plots to bring about Armageddon after a trip to Jerusalem. To do this, he kills 11 false prophets, taking sadistic pleasure killing his recent one by pinning him to a wall and choking him to death. Targeting a boy he believes to be a true prophet, Gates stalks the boy and kills his guardian angel, Owen Jarvis, followed by causing a car crash that kills the boy's mother. After successfully kidnapping him, Gates uses the boy as a meat shield when Agent Scully shows up and attempts to shred the boy and himself in a paper thresher to bring about the end of the world. Sadistic and dangerously delusional, Gates sought to bring about a "new age", which he described as "The sun will turn into darkness and the moon will turn into blood".
- "Hell Money": The Hard-Faced Man is the sadistic doctor of an organ harvest operation in San Francisco's Chinatown. Praying on immigrants' hopes and desperation, he rigs a lottery that gives the immigrants chances to earn money, but in truth is only a one-way ticket to death, with those who can't pay up burned alive in the crematorium. The Hard-Faced Man operates on patients while they're still conscious, and when arrested for his crimes, he has Detective Chao kidnapped and burned alive in the crematorium before he can testify against him.
- "Sanguinarium": Dr. Clifford Cox, alias Dr. Jack Franklyn, is a demonic doctor and a narcissistic warlock who, so that he can retain his youth and looks, takes over the minds of various surgeons and has them kill patients in horrific ways, such as draining a patient's blood via liposuction; nearly cutting a patient's head off with a laser; and melting a patient's face off. A nurse, Rebecca Waite, knows of Dr. Cox's true nature and goes to his home to kill him, but Dr. Cox's magically fills her with pins and nails, resulting in her death. At the end, Dr. Cox gets a new job using the alias Dr. Hartman.
- "Paper Hearts": John Lee Roche is an utterly evil child molester and Serial Killer who killed 16 little girls. He manipulated their parents to trust him, and then came back and kidnapped the girls at night. He plays sick mind games with Agent Mulder and tries to convince him that he took his little sister Samantha (whose disappearance was not explained), even though it's not true. He manages to escape from prison during the re-opened investigation and tries to take another girl. When Mulder catches them, he nearly shoots her. He doesn't regret his deeds at all and would continue if he could.
- "Familiar": "Mister Chuckleteeth" is a sadistic demon who is unleashed by a woman named Anna Strong who wanted revenge on her husband the security chief and thus unleashed a witch's curse that she intended to punish Chief Strong for his adultery. The demon however went rogue and started killing anyone close to the witch, including her children. The demon does this by disguising himself as the popular children's mascot Mister Chuckleteeth, luring a child named Andrew to the forest and then transforming into a hellhound to painfully and slowly maul him alive. "Mister Chuckleteeth" would later kill Anna's daughter, resulting in a sex offender being lynched by the townsfolk for the demon's crimes. "Mister Chuckleteeth" also tricked Chief Strong into killing Andrew's father Officer Eggers, and later mimicked Andrew to drive his mother off the road before killing her. His final confirmed victim would be the Chief himself.
- Conspiracy comic: Dr. Temple is a scientist tasked by the US government to create a deadly virus meant to wipe out a potential alien threat. Taking their plan further than it has to, Temple instead decides to infect humans with it and have it spread all across America, willing to wipe out billions of lives to stop the aliens. With his actions even disgusting his own colleagues, Temple even attempts to blow a CDC building up and kill hundreds to prevent a potential vaccine from being created.
