Meklord Emperor Genocide
The "Meklord Emperor Genocide" ("Machine Emperor Genocide" in Japanese) was an apocalyptic disaster that destroyed the world and brought humanity to extinction in Yu-Gi-Oh! 5D's.
Dr. Fudo's creation, Ener-D, has the power to accelerate the evolution of humanity and read the desires of humans. Approximately 200 years in the future humans discovered this, as well as found that Synchro Summoning can be used to control the Ener-D and accelerate its rotation. Thanks to it, humanity started evolving quickly, but humans started Synchro Summoning with the intention of evolving faster combined with dark, greedy desires, this caused the Ener-D, which was rotating too fast, to go out of control.
The Ener-D, now completely berserk, created the army of Meklord Emperors, with the order of killing humans. During the invasion, a scientist at that time discovered that using Synchro Monsters combined with Clear Mind causes the Meklord Emperors to stop attacking, because they only attack humans with negative desires that damage the Ener-D. The scientist took the identity of Yusei Fudo by modifying his face with a surgery and using a device that makes him think like Yusei in order to teach the remaining survivors this in hopes to stop the invasion. However, he discovered this too late, and the Ener-D reached its peak, causing it to explode together with the Meklord Emperors, as a result, all remaining survivors were killed. The scientist survived but his head device was damaged so he gave up hope in humanity.
Eventually the scientist, now under the name "Z-one", found three more survivors. They took the codenames Aporia, Antinomy, and Paradox. They spent many years making countless experiments to try and restore humanity, but their efforts were mostly futile and they all died due to their old ages except for Z-one, who connected himself to a machine that prolongs his life, leaving him as the survivor of mankind. Z-one then created cyborgs with the appearance and memories of his comrades (Antinomy's cyborg was given amnesia. Aporia was divided into 3 embodiments of despair, Lester being his child years, Primo as his late teen years, and Jakob as his elder years. Paradox was created to destroy the root source of Duel Monsters, Maximillion Pegasus). Z-one sent them into the past, in order to attempt to change history. Their plans included using Roman Goodwin to destroy the Ener-D through the Zero Reverse, killing Maximillion Pegasus so that Duel Monsters is not created which would result in the Ener-D never being discovered, stimulating Yusei's evolution so that he can stop the invasion, and destroying New Domino City using the Divine Temple in order to guarantee that a new Ener-D is not created.
Team 5D's interfered with their plan to use the Divine Temple to destroy the city and Yusei, with the help of Yugi Muto and Jaden Yuki stopped Paradox's plan on killing Pegasus and destroying Duel Monsters. During Yusei's Duel with Z-one, Z-one explained what happened in the future, not realizing that the entire city was listening. Thanks to it, the present is now aware of the situation, and Yusei was able to create a program called Fortune, whose function is to keep the Ener-D under control. Because of this, the future has changed, and the Meklord Emperor Genocide will never occur.