3W Institute Affair

The 3W Institute Affair (PROSE: Missy on Trial), also called the Nethersphere Plot, (GAME: Lost in Time) was the incident in which used the 3W Institute to create an army of weapons-grade Cybermen intended for the Twelfth Doctor.

Background
Though had escaped the Last Great Time War, (TV: Utopia)  returned to Gallifrey on the final day of the war after being embroiled in 's Ultimate Sanction. (TV: The End of Time) This last day ultimately ended when the planet, whilst besieged by the Daleks, was transported to a another dimension by the first thirteen incarnations of the Doctor. (TV: The Day of the Doctor) After being cured of his "little condition", the Master left Gallifrey in a "mutual kicking me out", eventually ending up on a Mondasian colony ship where he encountered his next incarnation,, in the company of the Twelfth Doctor. Refusing to allow Missy to stand with the Doctor as he defended the Mondasians from the Cybermen, the Master killed Missy after he himself was mortally wounded by her. Forced to regenerate, the Master returned to his TARDIS aware that he would lose most of his memory of this encounter. (TV: The Doctor Falls)

Missy decided to maneuver Clara Oswald into becoming the Doctor's companion, believing that Clara was just the right companion to attract the Doctor's interest and make it easier for Missy to emotionally manipulate him, (TV: Death in Heaven) showing him "the friend inside the enemy, [and] the enemy inside the friend." (TV: The Witch's Familiar) Ashildr believed that Missy placed the two together so that that the Doctor and Clara in tandem would become the Hybrid of Gallifreyan myth. (TV: Hell Bent) In 2013, Missy gave Clara the Doctor's phone number, claiming that it was a tech support line, leading Clara to meet the Eleventh Doctor. (TV: The Bells of Saint John, Death in Heaven) She then kept the Doctor and Clara together into the Doctor's twelfth incarnation by placing an ad in a newspaper for Mancini's Family Restaurant. (TV: Deep Breath, Death in Heaven)

Missy also founded the 3W Institute in order to create an army of weapons-grade Cybermen from the dead, (TV: Dark Water) whom she called her "Cyberdears", (PROSE: Meet Missy!) Needing to collect matrix slices that she had acquired in her previous incarnation, Missy travelled to London to receive them from her former wife, Lucy Saxon. (PROSE: The Unwanted Gift of Prophecy) Missy used the matrix data slices to create the Nethersphere, also known as Heaven and the Promised Land, where she uploaded dying minds to. This reality changed and rewrote the minds, removing their emotions before re-downloading them into their Cyber-converted bodies. (TV: Dark Water) Incidentally, the Doctor discovered that a ship of 29th century robots that had crashed in Nottingham of about 1190 had a programmed destination of "the promised land". (TV: Robot of Sherwood)

Missy went along the Doctor's timeline and greeted people who died in connection with him, (TV: Death in Heaven) such as the Half-Face Man, who had sought to enter the Promised Land, (TV: Deep Breath) and Gretchen Carlisle from the Good Dalek Incident. (TV: Into the Dalek) Finding this made her "a bit busy", Missy had Seb, an artificial intelligence, greet new people (TV: The Caretaker) whilst she secretly monitored the Twelfth Doctor and Clara, (TV: Flatline) as she did when Earth was saved from a solar flare by a forest that grew overnight. (TV: In the Forest of the Night)

The incident
In 2014, (COMIC: The Fractures) Clara was in a telephone conversation with Danny Pink, her boyfriend, (TV: Dark Water) when Danny was run over and killed by a milk float, driven by. (PROSE: Dismemberment) They were both teachers at Coal Hill School, where his death was subsequently announced by headteacher Frank Armitage, (TV: Dark Water) with Danny's name being added to the Coal Hill School Roll of Honours Board. (TV: For Tonight We Might Die)

At some point, Clara called the Doctor home, receiving him in her flat following a conversation with her grandmother. Clara suggested going to a volcano before she attempted to put a mood patch on his neck, but the Doctor realised what she was doing and turned it on her. Not realising she was the one drugged, Clara imagined being at the volcano and throwing all the Doctor's TARDIS keys into lava in order to blackmail him to save Danny. The Doctor refused, and Clara came out of her dream state after destroying all the TARDIS keys. (TV: Dark Water) Due to lingering memories of becoming a recluse after a betrayal from Clara, (COMIC: Four Doctors) the Doctor forgave Clara, and they duo went to find a way for her to see Danny again. Arriving at 3W due to the telepathic circuits, the Doctor and Clara were greeted by, who identified herself as a greeting droid and summoned Dr. Chang, who showed them the use of dark water in the mausoleum. Clara received a call from Danny, who was in the Nethersphere, and the Doctor and Chang left her to take it.

The Doctor and Chang discovered that the water tanks that held the bodies were being drained by Missy, who killed Chang and revealed that all the tanks held Cybermen, who were preparing to invade Earth. Escaping the building, which he discovered was St Paul's Cathedral, the Doctor tried to warn away nearby people, but Missy called out his warnings as insanity, and told him it was too late. The Doctor asked for her identity, and Missy revealed she was the Master, (TV: Dark Water) before she and the Doctor were apprehended by UNIT and brought aboard the plane Boat One, where the Doctor was made President of Earth to battle the Cybermen. Missy overpowered UNIT, killed Osgood, and attempted to kill the Doctor by blowing up the plane, but the Doctor survived his fall to Earth by skydiving into the TARDIS.

He travelled to a cemetery and reunited with Clara, who was comforting a converted Danny. Missy arrived and, as a "birthday present", gave the Doctor control of all the Cybermen. Missy planned to turn the Doctor into the leader of the new army, intending to prove that the two of them were not that different after all, believing that she had put him in the impossible position of either accepting control of the army and using it to "save" the universe or letting humanity die and conquer the universe as the Cybermen. However, reflecting on his past, the Doctor realised that he was just a man in a box who travelled around to help where he could, and then turned command of the army over to Danny, who led the Cybermen into the clouds, where they self-destructed and stopped the rainfall from converting the living. A devastated Missy told the Doctor he could find Gallifrey in its original location with coordinates she provided, but Clara threatened to kill Missy for what she had done, until the Doctor prepared to do it himself in order to "save [Clara's] soul". However, a rogue Cyberman disintegrated Missy instead, (TV: Death in Heaven) though the Doctor knew she had found a way to survive. (TV: The Magician's Apprentice) The Doctor realised that the Cyberman was his old friend the Brigadier and saluted him, fulfilling a lifelong wish of his old friend, who then flew away. (TV: Death in Heaven)

Aftermath
Malcolm Taylor headed the UNIT clean-up team which investigated the sight, designated Graveyard One, of 's confrontation with the Doctor and apparent death (PROSE: The Secret Diary of the Master) at the hands of the Brigadier. (TV: Death in Heaven) When his team discovered the Masterplan Journal, the Master's diary, he had its contents transcribed to a digital format and emailed them to Kate Stewart and the rest of UNIT Command. (PROSE: The Secret Diary of the Master)

Following the destruction of the Cyber-Army, the Doctor went to where Gallifrey would have been in his universe as Missy had promised only to find nothing, much to his dismay. Two weeks following the incident, Clara was contacted by Danny, who told her that the Nethersphere was dying and as the bracelet only had enough power to send one person back, resurrected the boy whom he killed. Meeting up together, the Doctor told Clara that he had found Gallifrey whilst she told him that Danny had returned before they agreed to go their separate ways. (TV: Death in Heaven) However, both the Doctor and Clara were attacked by dream crabs causing them to meet each other in a shared dream with Santa Claus. There they learnt that they had lied to each other and ultimately decided to resume their travels in the TARDIS. (TV: Last Christmas)

Missy later revealed her survival to both Clara and UNIT, using a time stop to halt Earth's planes to get their attention as she'd received the Doctor's confession dial and needed their aid to track him down, leading Missy and Clara to being embroiled in the Doctor's confrontation with Davros. The Doctor would later reveal to Clara he'd always suspected Missy had survived. (TV: The Magician's Apprentice) Missy would use the same method through which she had survived the 3W affair to save herself and Clara from extermination at the hands of the Daleks, revealing to Clara that the Doctor himself had employed it against Android Assassins. (TV: The Witch's Familiar) Following her containment in the Vault, (TV: Extremis) Missy would continue to try to win the Doctor's friendship back, through following a path towards redemption. (TV: The Lie of the Land, The Eaters of Light)

With her Zygon counterpart dead, (AUDIO: Narcissus) Petronella Osgood continued to work for UNIT and support Operation Double, refusing to disclose whether she was the human or the Zygon. The deceased Osgood's place was later taken by Bonnie; formerly the leader of the Zygon rebel group Truth or Consequences, she was convinced by the Doctor to back down from her attempt to break the ceasefire. (TV: The Zygon Invasion/The Zygon Inversion)

Whilst looking into memories of aliens for Into The Unknown, Professor Maxwell Grey met some young people who claimed to have memories of "metal men" outside of St Paul's in 2014. He theorised this was an example of the Mandela Effect, as older witnesses recalled a similar incident occurring in the 1960s. (PROSE: The Mandela Effect, Or Monsters on the Streets of London)