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The Battle of Canary Wharf was a major battle between humans and aliens in Earth history.
History
Origins
The Battle of Canary Wharf had its roots in the escape of the Cult of Skaro and the Genesis Ark into the Void from the Last Great Time War. This caused a crack in the universe, allowing travel between dimensions more easily than should have been the case after the demise of the Time Lords. (DW: The Age of Steel, Doomsday)
Beginnings
From the crack in the universe, the Parallel Earth Cybermen were able to travel from their dimension into ours, and infiltrated the planet in the disguise as the benign ghosts of deceased humans. This led to one of the more bizarre episodes in human history, as these "ghosts" came to become integrated into human society, to the point of even being featured in pop culture venues such as TV chat shows and soap operas (DW: Army of Ghosts).
After two months (three years in Parallel Earth time), the Cybermen suddenly appeared in their true form, occupying every landmass on the planet before breaking into houses and promising to upgrade all humans, commanded by the new Cyber-Leader. (DW: Army of Ghosts/Doomsday, TW: Everything Changes) The humans began a resistance campaign. While hampered by Cybermen armor being "bulletproof", their heavier weapons, such as rocket launchers, were effective against the Cybermen. (DW: Doomsday)
Simultaneously, the Cult of Skaro had exited the Void Ship with the Genesis Ark. The Cult, led by Dalek Sec, extracted information from a member of staff from Torchwood 1, and proceeded to communicate with the Cybermen via Dalek Thay. After a short round of commands and insults from both ends, both Dalek and Cybermen came to identify their respective adversaries (the Cybermen through a faux pas on the Dalek Thay's part, and the Daleks through recorded material of their universe's Cybermen), prompting a few more insults towards each other. The Cybermen proposed an alliance between the two races, as their technologies were compatible, and that together the two would "upgrade the universe". However, Thay rejected the proposal, and led to the Daleks to declare war (or in Dalek Sec's words, "pest control") on the Cybermen. (DW: Doomsday)
The battle
Following contact with the Daleks, the Cybermen began to convert Torchwood personnel, like Yvonne Hartman and Lisa Hallett in large numbers. (DW: Doomsday TW: Cyberwoman) These were, at least in some cases, not full conversions, with the brain removed and put in a Cyber-shell, but partial conversions where the Cybermen built over the human body beneath. (TW: Cyberwoman)
Torchwood was invaded by The Preachers from Pete's World, rescuing the Doctor. After learning more about the invasion from Pete Tyler, The Doctor "surrendered" to the Cybermen.
The Cybermen established a reluctant alliance with the human forces and some armed themselves with newly modified energy rifles. The Tenth Doctor entered the sphere chamber in order to learn about the Daleks' intentions and distract them. Using his sonic screwdriver, he triggered the doors to blast open.
The Cybermen-human alliance then rushed into the Sphere Chamber and the humans 'rescued' The Doctor and his companions from the cult. The Daleks began to panic as the Cybermen were overcoming them during the attack. However, shortly thereafter the Cult of Skaro developed an immunity to the parallel Earth energy weapons and their firepower was restored. All the humans survived this skirmish, but this was mainly because the Daleks identified the Cybermen as the greater threat out of the two and concentrated their fire on them. It was during this skirmish that the Genesis Ark was accidentally primed. The Daleks declared victory and began moving the Ark.
The Cult traveled to the main room in Torchwood Tower (Canary Wharf), barging open a door and shouting "exterminate!". Most of the Cybermen waiting for them, along with armed Torchwood personnel. A huge, though one-sided, battle ensued with the Cybermen opting to use their long range weaponry instead of their traditional electrified gauntlets. With heavy Cyber casualties following the clash, the Cyber Leader called for all troops in the greater London area to report to Torchwood Tower.
Dalek Sec elevated outside above the roof and opened the Genesis Ark, releasing millions of Daleks who, under Sec's command, proceeded to "exterminate all life-forms below", killing human and Cyberman alike. (DW: Doomsday)
During the battle, although the Cybermen's lasers had no effect on the Daleks, the Cybermen were able to destroy some by using their electrical attack from their hands to rip the Dalekanium domes off. Forefronts of the battle were Tower Bridge and the Tower of London, along with the town of Southwark. Although the Daleks only had a presence for several minutes, they were able to reach to as far as Aberdeen, where a group of Cybermen who decided to change their tactics, planning to ambush the Daleks. A single Cyberman was used as bait, when a group of Daleks arrived, the Cybermen attacked. However this advantage was short-lived as more Daleks turned the tables. (DWBIT: #17,Doctor Who: Battles in Time Daleks vs Cybermen Special)
The Tenth Doctor, his companions and The Preachers opened the Void, while the Cybermen and the Daleks rushed to stop them. A converted Yvonne Hartman stopped the Cybermen attack. The device sucked all the Daleks and Cybermen who had been in the Void back into it, and finally nearly sucking Rose herself in, but Pete Tyler teleported through the Void, grabbed her and teleported back to his parallel Earth. The TARDIS did not get sucked in, because of the various defences and emergency systems protecting it. It was here that Rose's family, Jackie Tyler, that universe's version of her father, Pete, and Mickey Smith had decided to stay, though Rose wasn't entirely willing in this.
The entire battle had lasted less than a day, but the Doctor commented on the aftermath that "so many" people died that day, and that the effects on Earth were devastating. (DW: Doomsday) Rose (and presumably Jackie) had been listed among those who died in the battle, fulfilling the beast's prophecy that Rose would die in battle, though not in the way implied. (DW: The Satan Pit)
Aftermath
Afterwards, of Torchwood 1's 823 personnel, there were only 27 known survivors. 467 were dead, with the rest numbered missing. humans converted into Cybermen using only materials from the main universe remained, unaffected by the Void and were interrogated and studied by the remaining Torchwood Institute personnel. (WEB: torchwood.org.uk) Between the active Torchwood 2 and 3 branches, there were only half a dozen remaining Torchwood staff. (DW: The Sound of Drums)
Lists of the dead and missing were compiled and made public. Among those officially declared dead was Rose Tyler (and, presumably, Jackie Tyler and Mickey Smith) (DW: Doomsday)
Members of Torchwood 3, including Jack Harkness salvaged all of the alien technology from the ruins of Canary Wharf. (TW: Fragments) Torchwood 3 became the main base of all Torchwood operations.
Known Torchwood survivors included Lisa Hallett and Ianto Jones, although Hallett's survival, partially converted into a Cyberman, was not immediately known by anyone other than Jones (TW: Cyberwoman). Jones (presumably hiding Hallett) subsequently travelled to Cardiff where he eventually ingratiated himself into Jack Harkness' Torchwood 3. (TW: Fragments). Jones hid Hallett within a secret area of the Torchwood 3 Hub for months in hopes of eventually reversing her conversion, but was unsuccessful and she was eventually terminated, making her the last known victim of the battle (TW: Cyberwoman).
The governments of the Earth denied the battle -- and presumably also the earlier arrival and ingratiation of the "ghosts" -- had ever happened and blamed the reports on mass hallucination caused by terrorists polluting the water supply with psychotropic drugs. (TW: Everything Changes) And it appeared life on Earth returned to normal. London would endure several more major high-profile incidents involving aliens in the coming months and years (DW: The Runaway Bride, Voyage of the Damned, Partners in Crime, The Sontaran Stratagem/The Poison Sky, The Stolen Earth/Journey's End, TW: Children of Earth), and by the end of the first decade of the 21st century the existence of alien life had become common knowledge to a large percentage of the populace (although there were many who refused to accept this reality (SJA: The Last Sontaran, TW: Children of Earth: Day One)).
By 2012, the Battle of Canary Wharf had become known as the Battle of Torchwood, and a publicly known event cited in news broadcasts. (DW: Fear Her)
By the 2050s Daleks and Cybermen had become common knowledge (SJA: The Mad Woman in the Attic).
Alternate timeline
In an alternate version of the battle, a squad of Cybermen were dispatched to the Canary Wharf Underground Station where they swiftly defeated a group of Torchwood Soldiers. They then fought through Canary Wharf Plaza and entered Torchwood 1's Artefact Room, where the Torchwood troops were being aided by Preachers. The Cybermen acquired stronger weapons to fight against the Daleks and moved to Parliament Square. They faced against a group of Daleks led by Dalek Sec and destroyed them. As he died, Dalek Sec announced that this is the end of the Daleks, and the Cybermen were victorius. (VG: Daleks v Cybermen)
It is unknown in this version of the battle, if the Cybermen won the overall battle, or if the Doctor sucked both armies into the Void.
Related later events
Some Cybermen remained, as they had been converted from Torchwood staff. Therefore, they were not contaminated by Voidstuff, and were not sucked into the Void. They began stealing Torchwood technology in their plot to reopen the Void and free the trapped Cybermen, but were defeated by the Tenth Doctor, Martha Jones and the Army. (NSA: Made of Steel)
Later, Davros was rescued from the Last Great Time War, and planned to destroy all possible timelines. This scheme meant that the walls of reality were breaking down. It allowed some of the Cybermen trapped in the Void to be released (through time) into the Victorian era. (DW: The Next Doctor) Other Cybermen, like those who arrived in 1851, also managed to escape the Void. They left their old universe behind and eventually became a space-faring race. (DW: The Pandorica Opens, VG: Return to Earth). A single Cyberman ended up deep within the oceans of Philjax III, in the year 9000 during the Daleks' battle with the Squeeth. (DWBIT: #9)
Torchwood files were stolen by an info-thief who used them to build a new army of Cybermen. They went to to invade the planet Centuria but were thwarted by the Tenth Doctor and Jayne Kadett. However, it was unclear whether they were actually totally defeated. (DWBIT: The Power of the Cybermen, Drones of Doom, Enemy Mine, Time of the Cybermen)