Unlike the rest of the world, the Opening has had less of an impact on the people of Japan. While there was still a massive loss of life, in rural Japan, most people continue the traditions of farming the land for rice to sustain the people.
Tokyo, however, was for a long time a lawless area, ruled by gangs who battled each other for territory, resources, and out of sheer boredom.
As Japan has never really had the abundance of firearms that exist in the US, it was not that far of a stretch for those who want to do violence to others to change from firearms to swords. After all, a sword doesn't need to be reloaded.
About 50 years ago, a man united the gangs in Tokyo and drove out those who wouldn't join. He was a master with the blade, and if the rumors were to be believed, impossible to kill.
Declaring himself Emperor of Tokyo, he offered his protection and the protection of his reborn samurai caste to the rural farmers, protecting them from bandits and rampaging monsters.
While the Emperor of Tokyo has never been shown to be a Gifted, the rumors persist; so much so, in fact, that a squad of Organization enforcers arrived to speak with the emperor. They verified that he was not a gifted. They also discovered that one of the samurai in his court, Kusinagi Tenchi, was.
Tenchi was ordered to go with the enforcers and represent the Empire of Tokyo in the Athenian Organization. Bowing to the Emperor, he left willingly.