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This is not war! This is pest control!
The Battle of Canary Wharf was one of the major battles 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
The sphere is not ours. The sphere broke down barriers between worlds, we only followed. Its origin is unknown.
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)
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 compatable, 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
Daleks, be warned. You have declared war upon the Cybermen.
The Cybermen established a reluctant alliance with the human forces and armed themselves with newly modified energy rifles. They then blasted into the sphere Chamber and 'rescued' The Doctor and his companions from the cult. 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 and the Cult of Skaro developed an immunity to the parallell Earth energy weapons. The Cult traveled to the main room in Torchwood Tower (Canary Wharf) and found most of the Cybermen waiting for them. 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. However, 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, 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)
The Doctor and Rose Tyler opened the Void, sucking 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. It was here that her 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 after math that "so many" people died that day, and that the effects on Earth were devastating. (DW: Doomsday) Rose (and presumably Jackie) had been listed amoung 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, acting on orders from Jack Harkness salvaged all of the alien technology from the ruins of Canary Wharf. (TW: Fragments) Harkness became the head of the Torchwood Institute (TW: Children of Earth: Day Four confirms), which changed its main base of operations to Cardiff.
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 Strategem/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 (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)
Related later events
The Doctor later discovered that the Daleks of the Cult of Skaro had escaped the battle and had transported to 1930s New York City, where an attempt at creating a Dalek/Human hybrid was made (DW: Daleks in Manhattan/Evolution of the Daleks). The last known survivor of the Cult, Dalek Caan, driven insane by returning to the era of the Last Great Time War, would later orchestrate a scheme that saw Earth relocated to the Medusa Cascade and an attempt by Davros to detonate the reality bomb (DW: The Stolen Earth/Journey's End).
Davros' scheme meant that the walls of reality were breaking down. It allowed some of the Cybermen that were trapped in the void to be released (through time) into the victorian era (DW: The Next Doctor).