The Antimatter Plant Explosions is an event that occurred on on April 13th, 2029. It was the final, and indeed successful, attempt to get rid of Radical-6. The virus otherwise would kill most, if not all, of humanity if nothing is done. It is mentioned by Tenmyouji in Phi END of Virtue's Last Reward. The explosions happened in the history leading up to that game, which takes place after the events of D-END: 1 and C-END: 1 in Zero Time Dilemma.
As mentioned during Virtue's Last Reward, it was believed that during the simulation at the Mars Mission Test Site in Nevada between December 25th and December 31st of 2028, the Radical-6 virus was released (although it is later revealed the outbreak started during the Decision Game in the Underground Shelter). In the early months of 2029, Radical-6 killed millions and then billions of people by causing them to kill themselves, leaving an estimated death toll of 2 billion.
The chaos eventually led to forms of transport being grounded to a halt. This killed additional people by starvation, most of whom weren't infected in the first place. The government then proceeded to contain the survivors in underground shelters.
On April 13th, 2029, all eighteen of the antimatter plants exploded simultaneously. The explosion was about 180,000 times as powerful as the atom bomb dropped on Hiroshima.
Though it is mostly a rumor and no one knows what really happened, many people, including Tenmyouji, believe that survivors from the pandemic from all over the world got in contact with each other by using radios. They decided that in order to get rid of the virus, purification was needed, so they destroyed all eighteen antimatter plants simultaneously in order to roast the surface of the Earth and eradicate the virus. However, Tenmyouji believes that the bombers were infected long before the plan and that they did it so that when they died, they took billions with them. He supposed it was the ultimate "if I die, you're coming with me" gesture.
The antimatter plant explosions killed the majority of humanity. After the Radical-6 pandemic, the ensuing chaos and the antimatter plant explosions, approximately 6 billion were dead.
The antimatter plant explosions were successful in getting rid of the virus, albeit with major side effects. Debris was spewed into the air and stratosphere, where it joined with smoke and ash from all the fires. This blocked the sun for seven years, as well as creating a nuclear winter. Plants withered and animals died by the millions. The few humans who were left banded together to survive during these rough times.
Eventually, life on Earth recovered around 2036, with plants growing back and livestock, which weren't already killed repopulating once again. There are still visible after effects though, such as the Earth appearing red from space, due to the ash preventing blue and green light from escaping, since their wavelengths are too short, allowing only red light to pass through. This makes Earth look red from outer space. The Earth also became a wasteland.
Failed attempt to stop the Antimatter Plant Explosions
As organized by Crash Keys, Sigma Klim and Phi send their consciousnesses from January 27th, 2074 to December 25th, 2028, in order to infiltrate the Mars Mission Test Site, and stop Radical-6 from being released. This would stop the antimatter plants from ever exploding, saving humanity. They fail however, likely due to the absence of ?, or a failed attempt by ?.
In order to create another timeline and another chance at stopping Radical-6, Crash Keys created the Nonary Game: Ambidex Edition, in order to send Sigma's and Phi's consciousnesses to the past. Sigma's mind would be his 67-year-old consciousness, although due to his consciousness swap, all he knows is that he lost both his arms and his left eye while trying to save a woman.
The attempt to send Sigma's consciousness back to the past (2028) with knowledge of the horrible future of 2074 was successful.
After the Ambidex Game finished, in the non-canon "Another Time End", ?, in Kyle Klim's body, spoke with Akane Kurashiki, who told ? that ? needed to go to the past to assist Sigma and Phi by stopping Radical-6 and that ? was the only one who could save Earth and prevent the reactors from exploding.