Returning to Gallifrey after making an alliance with the Cybermen at the end of the universe, Rassilon created an alternate timeline as he enabled the Cybermen to embark on a campaign to seize all of time and space. To that end, the Cybermen made incursions in numerous time periods, affecting the first thirteen incarnations of the Doctor, changing history. (COMIC: Supremacy of the Cybermen)
At the end of the universe, a group of Cybermen living within an asteroid were found by Rassilon after he was banished from Gallifrey. Rassilon saw the potential in allying with the Cybermen and let himself be converted into a Cyber-Leader. With Rassilon's assistance, the Cybermen attacked and conquered Gallifrey, and rewrote history with the Time Lords' technology to keep the Doctor occupied at Rassilon's insistence.
In the new timeline, Cyber-Silurians seeded the universe with ark ships containing cybertechnology. The Eleventh Doctor attempted to stop the launch of the arks, but he was captured and assimilated into the Cyberiad.
After the CyberKings captured nearly all Sontaran cloning worlds and caused the extinction of the Rutan Host, the Tenth Doctor, Gabby Gonzalez and Cindy Wu were taken to the Sontaran-Prime on Sontar by some of the last surviving Sontarans. The Doctor tried to protect Sontar from the CyberKings, but was unable to stop an ark from converting Sontar on a planetary scale. The Sontaran cloning factories were then altered by the Cybermen so that they produced an endless supply of Mondasians to convert.
The Cybermen conquered countless more planets, including Alpha Centauri, Karn, (COMIC: Supremacy of the Cybermen) Skaro, (COMIC: Prologue: The Fifth Doctor) and even invaded the Matrix during the Sixth Doctor's trial on Space Station Zenobia. (COMIC: Prologue: The Sixth Doctor) The Daleks were destroyed, (COMIC: Supremacy of the Cybermen) resulting in the Cybermen taking their place in the Last Great Time War. (COMIC: Prologue: The War Doctor) Earth was completely taken over by Cybermen in 2006. After Rose Tyler was converted and Jack Harkness was killed, the Ninth Doctor tried to destroy the Cybermen. Instead, he was infected with nanobots and cyberconverted. (COMIC: Supremacy of the Cybermen)
The First Doctor was captured at 76 Totter's Lane in 1963 and tried to get his granddaughter Susan away from the Cybermen, (COMIC: Prologue: The First Doctor) the Second Doctor was converted into a Cyber-Leader at the Moonbase in 2070, (COMIC: Prologue: The Second Doctor) a time distortion brought a cyberfication machine into the Third Doctor's laboratory which converted the Master. (COMIC: Prologue: The Third Doctor) and the Fourth Doctor found himself surrounded by Cybermen when K9 was converted. (COMIC: Prologue: The Fourth Doctor)
The Fifth Doctor and Peri Brown were pursed by Cybermen on Skaro. (COMIC: Prologue: The Fifth Doctor, Supremacy of the Cybermen) The Seventh Doctor attempted to destroy the cyber-fleet with nemesis mines, but he was attacked by a cyberconverted Ace. (COMIC: Prologue: The Seventh Doctor, Supremacy of the Cybermen) The Eighth Doctor and Josie Day were captured by Cybermen and Cybermats on a spaceship. (COMIC: Prologue: The Eighth Doctor)
At the end of the universe, the Cybermen used looms to siphon the regenerative energy from Time Lords into the Eye of Harmony. They planned to use the Eye of Harmony to shape the formation of the next universe, making a reality perfectly suited to the Cyberiad. The Twelfth Doctor came to Gallifrey and confronted Rassilon and the Cybermen. When the Doctor was forced into a loom, the Cyber-Controller betrayed Rassilon and put him in a loom as well. The Doctor and Rassilon used their combined willpower to influence the energy being pumped into the Eye of Harmony and instead of regenerating the future, they regenerated the past. Everything the Cybermen had done was reversed and their supremacy over all of time and space was wiped from the memory of the universe.