In an alternate timeline, Rassilon, following his exile from Gallifrey by the Twelfth Doctor, discovered an asteroid colony of Cybermen at the end of the universe. Proposing an alliance, Rassilon enabled the Cybermen to embark on a campaign to conquer Gallifrey and, by extension, all of time and space. In addition, the Cybermen ensured that the Doctor's first twelve incarnations did not intervene in their ultimate conquest, by forcing them into various scenarios where the Cybermen were too powerful to be defeated.
Following his exile from Gallifrey by the Twelfth Doctor, Rassilon discovered an asteroid colony of Cybermen at the end of the universe. Inspired by the Cybermen's will to survive even at the end of N-Space, and after discussions with the Cyber-Leader, Rassilon proposed an alliance with the Cybermen, which they accepted. The Cybermen converted Rassilon into the "Cyber-President", and together, they forged the Gallifreyan Cyber Fleet and launched an invasion of the Capitol on Gallifrey. Sometime during the invasion, Rassilon hijacked the Eye of Harmony, killing all of Gallifrey's TARDISes and preventing the Time Lords from launching a fleet of Battle TARDISes in defence.
While the Gallifreyan Cyber Fleet attacked the Capitol, both on ground-level and in the air, Rassilon and a squad of Cybermen transmatted directly into the Capitol, and killed numerous Time Lord soldiers and the Lady President. While Rassilon ordered the Cybermen to capture the Time Lords in the Capitol and take them to the Eye of Harmony's chamber, the General, who was a part of the Time Lord squad guarding the Lady President, teleported into the Undercity and rounded up several surviving Time Lords into the Tomb of Rassilon, the only area on Gallifrey that the Gallifreyan Cyber Fleet could not breach.
Sometime between Rassilon's initial encounter with the Cybermen and their invasion of Gallifrey, Rassilon gave the Cybermen the power to conquer all of time and space with Time Lord technology, particularly to keep the Doctor's first twelve incarnations occupied so that they could not intervene with the Cybermen's ultimate conquest. (COMIC: Supremacy of the Cybermen)
Cyber-conquest of prehistoric Earth
On prehistoric Earth, the entire Silurian race were converted into Cyber-Silurians and tasked with re-engineering Silurian Arks into Cyber-Arks in order to seed the universe with Cyber-Technology before humanity could begin evolving. The Eleventh Doctor and Alice Obiefune explored one of the Cyber-Arks but were attacked by several Cyber-Silurians. Alice escaped and the Doctor was upgraded into the Cyberiad, however, the Doctor used his new cyber-connection to disable the emotional inhibitors of the Cyber-Silurians; in response, the Cyberiad terminated all the Cyber-Silurians and launched the Cyber-Arks, much to the Doctor's distress. (COMIC: Supremacy of the Cybermen)
Further Cyber-attacks on Earth
Despite these events, Earth was also attacked at other points in time. One such attack occurred in November 1963, when the First Doctor was captured by three Mondasian Cybermen outside his TARDIS at 76 Totter's Lane. (COMIC: Prologue: The First Doctor)
In 2006, the Cybermen launched a full-scale invasion of Earth. By seeding Earth's atmosphere with an airborne, microscopic techno-virus, the Cybermen transformed Earth into the Cyber-Earth and converted humanity into Cyber-Warriors in only three days. The Ninth Doctor, Rose Tyler and Jack Harkness rescued Jackie Tyler from a large Cyberdog and crashed their flyer into St Paul's Cathedral. In an attempt to recover the Doctor's TARDIS, the console exploded and the TARDIS began imploding. Whilst the Doctor and Jackie escaped back to the flyer, Rose was suddenly cyber-converted and killed Jack; when he used his sonic screwdriver on Rose, the Doctor was attacked by the Cybermen's techno-virus and was partially converted. In a final desperate attempt to stop the Cybermen using the virus to convert and invade other planets, the Doctor attempted to rupture the Heart of the TARDIS and destroy the Earth. However, the power was suddenly diverted to the Eye of Harmony on Gallifrey by the Cybermen, who had seized control of the Eye during their invasion of Gallifrey at the end of the universe. The cyber-converted Rose then broke into the TARDIS and prepared to kill the Doctor and Jackie. (COMIC: Supremacy of the Cybermen)
Moonbase Laika and the Matrix
Elsewhere in time, the Second Doctor was partially cyber-converted on Moonbase Laika (COMIC: Prologue: The Second Doctor) by a force of Cybermen of the "Late" CyberFaction. (COMIC: Supremacy of the Cybermen) During the Sixth Doctor's trial against the Valeyard on Space Station Zenobia, the Doctor and Melanie Bush were confronted by an advanced squad of Cybermen who had gained control of the Matrix. (COMIC: Prologue: The Sixth Doctor, Supremacy of the Cybermen)
The Last Great Time War
Additionally, the Cybermen also actively chose to erase the creation of the Daleks from history (COMIC: Supremacy of the Cybermen) by conquering Skaro. Eventually, the Cybermen diverted the Fifth Doctor's TARDIS to Skaro, where a Nomad Cyber-Leader ordered a CyberIsomorph to kill the Doctor and Peri Brown. (COMIC: Prologue: The Fifth Doctor)
With the Daleks erased from history, (COMIC: Supremacy of the Cybermen) the Cybermen continued to grow in dominance, to the point that the Time Lords engaged the Cybermen in the Last Great Time War. (COMIC: Prologue: The War Doctor) Unlike in the original timeline, (TV: The Day of the Doctor) the War Doctor used the Moment to eradicate both the Cybermen and Gallifrey. (COMIC: Prologue: The War Doctor) However, his actions would prove to be in vain, as the Cybermen not only survived the war, but grew even stronger from it.
Destruction of the Sontaran Empire
By the 24th century, the Cyber-Empire of the Cybus Cybermen had successfully annihilated several of the universe's most powerful species and planets, including the Rutans, Alpha Centauri, and nearly the entire Sontaran Empire. This was largely due to the Gallifreyan portal technology the Cybermen had acquired, which the Tenth Doctor believed had ceased to exist following the Last Great Time War; this granted the Cybermen the ability to instantly deploy entire armies of Cybermen onto a planet, allowing for invasions of far greater efficiency than with traditional invasion fleets.
The Tenth Doctor was captured, along with Gabby Gonzalez and Cindy Wu, from the now-empty Cosmomart by the Last Great Sontaran War Fleet to serve as the Sontarans' field marshal against a Cyberman invasion of Sontar, the last remaining world in the Sontaran Empire. After causing the Imperial Flagship to crash on Sontar, a huge army of Cybermen emerged from numerous Gallifreyan portals above the planet's surface and commenced their attack, with the aim of gaining control of the Sontaran cloning factories to produce an infinite supply of Mondasians for conversion. In an attempt to gain an advantage, Gabby and Cindy distracted one of the attacking CyberKings by flying a stray Sontaran scout ship near it; when the Doctor believed that Gabby and Cindy had been killed, he crashed his own Sontaran scout ship into the CyberKing's control throne. After wiring himself into the CyberKing's throne, the Doctor, consumed with rage, destroyed the other two CyberKings, only to be intercepted by a Cyber-Ark, which commenced full planetary conversion of Sontar. (COMIC: Supremacy of the Cybermen)
Further attacks on the Doctor
The Cybermen also attacked the Doctor's incarnations at unspecified points in time. The Third Doctor was attacked by a time distortion during a fight with the Master, causing a Cyberfication machine to appear and convert the Master into a CyberNomad. (COMIC: Prologue: The Third Doctor) Additionally, the Fourth Doctor was trapped in a mansion by numerous Cybermen and a Cyber-Leader; when he ordered K9 to attack them in defence, K9 was converted and turned on the Doctor. (COMIC: Prologue: The Fourth Doctor)
Elsewhere, the Seventh Doctor infiltrated an Isomorph Cyber-Fleet and prepared to destroy it with nemesis mines, only to be confronted by a cyber-converted Ace. (COMIC: Prologue: The Seventh Doctor) Furthermore, the Eighth Doctor and Josie Day, after finding the Doctor's TARDIS being attacked by a swarm of Cybermats, were captured by several Cybermen, (COMIC: Prologue: The Eighth Doctor) resembling those that attacked the Dreadnought in the original timeline, (COMIC: Dreadnought) that chanted "save!" (COMIC: Prologue: The Eighth Doctor)
The Age of the Cyberiad
During the final days of the universe, the Twelfth Doctor's TARDIS crashed on Karn, after the Twelfth Doctor failed to contact Gallifrey and inform the Time Lords of the vortex tsunamis appearing throughout the Time Vortex as a result of the Cybermen's conquests across time and space. When the Cybermen launched an attack on Karn, Ohila allowed the Doctor to use the Sisterhood of Karn's backdoor to reach Gallifrey, where the Doctor confronted Rassilon and the Cybermen. Eventually, a team of Gallifreyan soldiers destroyed Rassilon's Cyberman escorts and teleported the Doctor to the General in the Tomb of Rassilon. Allowing Rassilon inside to understand the situation further, the three Time Lords travelled to the Eye of Harmony, where the Cybermen were using Looms to harvest regeneration energy from numerous captured Time Lords and feed it into the Eye.
After the Cybermen forced the General into a loom, Rassilon revealed his plans: to ignite the Eye of Harmony at the moment the universe ended and use the regenerative energy inside the Eye to regenerate N-Space into a reality where the former Lord President of Gallifrey would be "a god, worshipped by all." The Cybermen then betrayed Rassilon, forcing him and the Doctor into looms, and the Cyber-Controller revealed itself as the true leader of the Cybermen.
The Cyber-Controller revealed to the Twelfth Doctor that the Cybermen intended to perform Rassilon's plan themselves to regenerate N-Space into the Age of the Cyberiad, a universe controlled by the Cybermen from its very beginning. When Rassilon's regenerative readings fluctuated, the Doctor was converted to serve as an alternative means of focusing the regenerative energy in the Eye of Harmony. However, the two Time Lords were able to to unite mentally within the Cyberiad, and together, they reversed the flow of the regenerative energy through the Eye to regenerate the universe to its form prior to Rassilon's initial encounter with the Cybermen, erasing the Cybermen's conquests of time and space from history.
Although most of the Doctor's incarnations did not remember their involvements with this timeline, the Ninth, Tenth and Eleventh Doctors remembered their encounters with the Cybermen during this version of history, but were confused as to how they had been resolved. (COMIC: Supremacy of the Cybermen) Additionally, Rose Tyler remembered her cyber-conversion from this timeline after Addison Delamar attempted to extract her memories. (COMIC: The Bidding War) The Ninth Doctor enlisted the assistance of the Silurians in preventing Rose from suffering an extreme mental shutdown as a result of these memories, and she was eventually cured. (COMIC: The Lost Dimension)
Furthermore, the Twelfth Doctor retained complete memories of the entire alternate timeline despite its erasure. While his TARDIS departed Gallifrey once more, the Doctor contemplated if Rassilon was once again alone at the end of the universe, and if he also remembered the entire timeline. (COMIC: Supremacy of the Cybermen)