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 " . History . 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 Summon ing 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 Emperor s , with the order of killing humans . During the invasion , a scientist at that time discovered that using Synchro Monster s 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 .