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- You may be looking for the secretive Gallifreyan organisation.
The Central Intelligence Agency or CIA was an international intelligence branch of the United States government.
In 1947, the CIA retro-engineered the Nedenah spacecraft which had crashed near Roswell. As a result, in 1948, when the Nedenah came to rescue the vessel, the CIA shot them down. Because the Americans were able to drive them off, the Nedenah stopped trying to rescue the captured pilot. In 1970, the CIA captured the Brigadier at Roswell with the Nedenah, and destroyed England's cobalt reserves in order to thwart the Waro attack at Roswell. The Americans underestimated them, and believed that they could beat the Waro, and that the CIA would replace UNIT. (PROSE: The Devil Goblins from Neptune)
In the 1960s, the CIA captured a Dimensional Phase Multiplexer from a spaceship the US military had shot down. Two aliens from the ship, Melody Quartararo and Parker Theroux, joined the CIA in an attempt to regain the Dimensional Phase Multiplexer. (PROSE: Drift)
In the 1970s, Agent Paul was sent to investigate the Remoraxian presence in the UK. He activated a bombing that would utterly destroy the country, as put into motion by the CIA. (COMIC: In With the Tide)
In 1999, the CIA allied itself to Intercom to find an alien, and they captured Turlough. Unknown to the CIA, Intercom was a cover for the Jex, who intended to conquer Earth and repopulate it with human-Trions hybrids for slaves. Worse, the Jex had been pursued by the Canavitchi, their former slaves who used the Sons of Nostradamus, mystical terrorists, to strike UNIT, the CIA and Intercom. The Canavitchi planned to let the Jex attack the Earth and destroy the planet so the Jex fleet would be anihilated. The CIA had to help the Fifth Doctor, Tegan, Turlough and UNIT to arrest not only the Sons of Nostradamus, but also the Jex spearhead and their human accomplices at Intercom. They were able to shield Earth, using the satellite network, protecting it from the space battle between Jex and Canavitchi. (PROSE: The King of Terror)
In 2001, the CIA attempted to save the Earth from the Kulan invasion without UNIT involvement. They tracked down Fitz Kreiner and Sa'Motta, who were suspected of being alien agents. (PROSE: Escape Velocity)
In 2002, the CIA attempted to take control of the Naryshkin Institute experiment in Russia because they believed that the Institute had created a black hole to travel in time, based on spy planes sent into Siberia which registered temporal distortions. (PROSE: Time Zero)
When the Cardiff Space-Time Rift fractured resulting in time slips across the world, the CIA was one of several organisations that noticed the strange appearances that were occurring worldwide and asked if it had anything to do with Torchwood. (TV: End of Days)
In 2011, CIA agent Rex Matheson was in a terrible car accident that had him impaled by a pole, but because of Miracle Day he survived. His fellow agent Esther Drummond investigated Torchwood at the CIA archives, where she came across Captain Jack Harkness. After an attampt on Jack's life by a suicide bomber also working for the CIA, Jack had to give Esther retcon to make her forget what she had seen. Meanwhile, Matheson arrived at Gwen Cooper's home in Wales. Jack also made his way there, just as a mysterious black helicopter attempted to blow up the house. Rex, Jack, Gwen, her husband Rhys and her newborn daughter escaped from the attack in a car. Matheson contacted the police and arrested Torchwood for Rendition to the USA. (TV: The New World)
Rex Matheson and Lyn Peterfield accompanied Jack Harkness and Gwen Cooper back to America on a plane. Unbeknownst to everyone else, Lyn was ordered to remove Jack, as the CIA had somehow learned Jack was mortal. She slipped arsenic into his cola, which Jack then drank. Rex later discovered what had happened, created an antidote to the poison, whilst Gwen Cooper apprehended Lyn. Meanwhile, at CIA headquarters, Esther discovered her identity had been removed and that she was being framed. She escaped using the identity of Charlotte Wills and went to the airport to warn Rex. On arrival at the airport Lyn was put in handcuffs but given the key without Rex knowing. Esther called Rex and warned him the CIA was against them just in time for Rex to defend himself from a surprise attack by Lyn and some other agents. During the fight, Lyn had her neck broken, but survived due to Miracle Day. Rex, Jack and Gwen fled the airport and met up with Esther who arrived in a blue Mini. They drove from the CIA agents and Lyn, whose head had been rotated 180 degrees. (TV: Rendition)
Convinced that the CIA had turned against him, Rex broke into Brian Friedkin's house and interrogated him at gunpoint, learning about the mysterious group that had ordered Jack and anyone who had made contact with him be eliminated. (TV: Dead of Night)
After Rex called Doctor Vera Juarez's brother, Friedkin tracked him to Angelo Colasanto's mansion and tried to assassinate him, Jack and Gwen. However, Rex tricked Friedkin into confessing to him and broadcast the truth to arriving CIA agents through the Eye-5 lenses. Friedkin and his men were arrested, but he blew himself up out of fear of the Three Families. Rex and Esther were returned to work with the CIA as a result and the Torchwood team started working with the CIA. After the discovery of a null field generator, Gwen was deported since Jack refused to cooperate and Jack had Esther and Rex help him escape with a vital piece. While Esther went with Jack as he was seriously wounded, Rex stayed with the CIA to help track the Three Families, not knowing that Charlotte Wills was blocking their efforts. (TV: End of the Road)
Using CIA resources Rex helped track the locations of the Blessing to Shanghai and Buenos Aires. Rex was given permission to work undercover by Allen Shapiro to avoid attention from the Families, but Wills found out anyway when he had to sign to retrieve the case of Jack's mortal blood Esther brought to Buenos Aires. The CIA sent the Argentinian army to help Rex and Esther and tracked Wills as the mole before she blew up Shapiro and Noah Vickers to prevent the truth from getting out. Esther died in the effort to reverse the Miracle and at Esther's memorial service, the team learned of Wills' duplicity from a post-mortem email from Vickers. Wills killed Rex before being gunned down herself, but Rex somehow ended up with Jack's immortality and was resurrected. (TV: The Gathering, The Blood Line)