- Secret Organizations
- The Agency
- Secret Government agency (Season 2 episode That Waldo Moment)
- The Atlantis Program
- The Luna Stone is a mythical alien rock that was supposedly found on the moon during Apollo 11. This stone is credited as the power that actually unlocked time travel. It's transdimensional powers, and the very idea of multiple dimensions, created such organizations as the Luna Society, the Atlantis Program, and many others.
- The B.R.O.T.H.E.R.H.O.O.D.
- A secret organization that battles The Man's influence.
- The Birdwatchers
- Mrs. S's old network (Season 2 episode Governed by Sound Reason and True Religion)
- Black Book
- Secret government program and predecessor to Project Blackwing (Season 2)
- Brotherhood of the Cruciform Sword
- The Brotherhood of the Wolf
- Secret society that is working to undermine public confidence in the king and ultimately take over the country.
- The Brotherhood
- But what was strange was that although Goldstein was hated and despised by everybody, although every day and a thousand times a day, on platforms, on the telescreen, in newspapers, in books, his theories were refuted, smashed, ridiculed, held up to the general gaze for the pitiful rubbish that they were - in spite of all this, his influence never seemed to grow less. Always there were fresh dupes waiting to be seduced by him. A day never passed when spies and saboteurs acting under his directions were not unmasked by the Thought Police. He was the commander of a vast shadowy army, an underground network of conspirators dedicated to the overthrow of the State. The Brotherhood, its name was supposed to be.
- Secret brotherhood of dirty joke writers. An army of dedicated warriors marching on the strongholds of prudery. Knights Templar with a just and joyous mission.
- Doctor Who Virgin New Adventures Psi Powers arc.
- Causal Adjust
- Also known as The Editors - secret group that tries to kill Ray and his friends.
- The Center
- Covertly protects the people of Earth from supernatural threats.
- Clone Club
- Nickname for Allison, Cosima and Beth's (and then Sarah)'s little clone group, first mentioned (Season 1 episode Natural Selection)
- The Club
- The club where men tell each other strange and unusual stories (Story: The Breathing Method)
- The Collectors
- Group of object-seekers led by Arlene Conroy, the manager of the Sunshine Motel.
- The Commission
- Organization tasked with the preservation of the time continuum through manipulation and removals. (Season 1 episode Number Five)
- The Company
- Clandestine organization that locates and tracks evolved humans.
- The Consortium
- Secret society created to build a time machine to prevent the Manhattan Project, and thus the atom bomb, from ever existing by deporting Einstein. (Season 1 episode Once in a Lifetime)
- The Cosmos Club
- Samantha's fun-loving cousin Serena is a member of the Cosmos Club.
- The Cosmos Cotillion
- Samantha's fun-loving cousin Serena is a chairperson of the Cosmos Cotillion.
- The Council of Wizards
- Mystical organization sworn to protect the realms from the Seven Deadly Sins.
- The Dark Ones
- A race of godlike beings (Season 1 Episode Books from Beyond)
- The Daughters
- Group of nomadic survivors in the future led by Leland Goines' daughter Jennifer. (Season 2 episode Primary)
- The Division
- A secret government agency that hunts down and experiments on people with psychic abilities since 1945.
- Esoteric Order of Dagon
- The primary religion in Innsmouth.
- The Eye
- Keepers and protectors of real magic.
- The Firm
- Secret organization that employs Turbulence Experts.
- FOWL (Fiendish Organization of World Larceny)
- The Friends of Humanity
- Organization that sends a message into to the past.
- The Grail
- A secret organization controlling the governments of the world and protecting the bloodline of Jesus.
- The Guard
- Secret organization in Haven, first mentioned (Season 3 episode Over My Head)
- The Hand
- An ancient and powerful ninja clan of paramilitary and ideological nature with the ultimate goal to gain immortality, according to Stick. (Season 2 episode Guilty as Sin)
- The Harvest
- Dr. Kevin Christie's secret organization of agents made up of children that he kidnapped and raised to follow his will. (Season 1 episode Talking Hurts)
- The Illuminati
- Secret society seeking to rejoin the halves of the Triangle of Light.
- New record added 6/25/2022
- Stephen asks if they’re taking him to see HYDRA. They’re not - he’s going to see the Illuminati, a secret group his alternate self created on Earth-838.
- The Invisibles
- A secret society known as the Invisibles recruits three outcasts to help them with their aim of infiltrating the U.S. government. (Episode The Invisibles)
- The Karori Zombie Society
- The Keepers
- Neutral, secretive group striving to maintain balance within opposing religious groups in the City.
- The Knights of Serbia
- Ancient cult dedicated to hunting the undead. (Season 3 episode Wuffenloaf)
- Knights of the Circular Object
- The Knights of Thunder
- One of the many secrete organizations Ron is affiliated with. They'll kill you just for printing their name.
- The Legacy
- Secret society that protects humankind from occult dangers.
- The Legion
- Cabal dedicated to finding all of the Objects and hiding them for the protection of humanity.
- The Lords
- From the poetry of Jim Morrison. Described during an interview as: "A romantic race of people who have found a way to control their environment, their own lives. They are somehow different from other people. "
- The Lower Hutt Vampire Witch Club
- The Luna Society
- The Luna Stone is a mythical alien rock that was supposedly found on the moon during Apollo 11. This stone is credited as the power that actually unlocked time travel. It's transdimensional powers, and the very idea of multiple dimensions, created such organizations as the Luna Society, the Atlantis Program, and many others.
- The Magi
- The descendants of the pharoah's secret bodyguards.
- Top-secret organization established to monitor and police alien activity on Earth.
- The Messengers
- Mysterious group of time travelers. First appearance. (Season 1 episode Arms of Mine) Named revealed. (Season 2 episode Year of the Monkey)
- Millenium Group
- Started out as a Christian sect at the end of the 1st century AD, eventually morphing to a private investigative firm liaising with law enforcement organizations.
- The Mondoshawans
- Guardians of the universe.
- NAH
- Nihilistic (or Nameless) Anarchist Horde.
- Order of Aurelius
- An elite sect of vampires.
- Order of the Phoenix
- Secret organization founded by Albus Dumbledore.
- Organization of Super Spies (OSS)
- US based international espionage and defense agency.
- The Pentaverate
- The world's oldest and most effective secret society. A benevolent, fully sequestered secret society of five men, who, since 1347, have been experts in their fields. (Season 1 Episode 1)
- Prodigium
- The name means: "A warning of monsters". Mission: Recognize ' Contain ' Examine ' Destroy.
- Programs Groups
- The personal agents and spies of the High Programmers at the apex of Alpha Complex society.
- The Red Party
- Murderous secret society The Red Party infiltrates the International Scientists Conference held in the city of Metropolis.
- Rittenhouse
- Secret organization at the heart of the mystery of the show.
- S.A.V.E.
- Secret organization that tracks down and eliminates evil in the world.
- S.E.S.
- Smallfoot Evidentiary Society.
- S.H.A.D.E.
- Jake Peralta: My dream job is spy falsely accused of betraying his country, forced to work alone to clear his name by taking down the mysterious organization that framed him known only as S.H.A.D.E. (Season 7 episode Captain Kim)
- Seal Club
- Idolizes the Outdoors but is unsure what plants and animals actually look like.
- The Seance and Science Brigade
- Informal group dedicated to applying empirical reality to paranormal phenomenon. The group that originally named Area X They called it "Active site X"
- Also known as The Light Brigade (Saul's nickname), also known as The Seeker and Surveillance Bandits (The biologist's nickname)
- Secret Order of Dirty Joke Writers
- Secret organization, adapted from the short story by Richard Matheson. (Season 8 episode The Splendid Source)
- Section 13
- Secret government organization led by Capt. Black.
- Sentries of the Last Cosmos
- The Shadow Directory
- Doctor Who Virgin New Adventures Psi-Powers arc.
- The Shop
- Shadow organization secretly controlling the government agency DSI, also known as Department of Scientific Investigation.
- Shadow organization secretly controlling the government agency DSI, also known as Department of Scientific Investigation.
- The mysterious shadow organization that's secretly funding Dr. Angelo's research, referred to as the puppet masters.
- The Society of Crossed Keys
 - When Gustave escapes from jail, he calls Ivan at the Excelsior Palace to formally request the special services of The Society of Crossed Keys.
- Spy for Another Alpha Complex
- The Syndicate
- Jake comes up with a more fun way to get pregnant, calling Amy and disguising his voice, telling her that her husband has been kidnapped by The Syndicate and she needs to go to the copy room. (Season 7 episode Trying)
- Talmasca Caste
- A secret society created in AD 758 to watch over and keep track of the paranormal, in particular, witches, spirits, werewolves and vampires. Also known as the Talamasca Caste and the Order of the Talamasca.
- Time Masters
- Organization officially tasked with protecting the timeline.
- The True Knot
- Rose the Hat's gang that instills fear in their shining victims before they feed on their steam.
- W.H.O.
- Weird Happenings Organisation.
- The Wanderers
- Group of Wayward Pines residents that have removed their chips and now wander around town at night.
- Group of Wayward Pines residents that have removed their chips and now wander around town at night.
- Warriors of Light
- Since the time immemorial, the knights who call themselves the Warriors of Light have been chasing witches and sorcerers who torture humans.
- The Watchers
- The group that keeps tabs the immortals.
- Wellington Vampire Association
- The Wobblies
- A group that consists entirely of spies for other groups.
- Zhat Vash
- Tal Shiar myth - Before the Tal Shiar, there was the Zhat Vash, the mask worn by another, far older cabal that operates without regard for treaty or jurisdiction, and not just in Roman worlds, but in the Klingon Empire, the Gorn Hegemony, even the Federation itself. (Season 1 episode Maps and Legends)
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