Tokyo was the de-facto capital of Japan. It was the home of Tony Delgatto's son Will Delgatto, his wife and daughter, Yoko. Before the 2012 apocalypse, Tony and his music partner, Harry Helmsley, were en route to Tokyo for their next musical event on board the Genesis. During the apocalypse, the city was hit by a massive earthquake, which presumably killed Will and his family, before the island of Japan was swept by a mega-tsunami during the Worldwide Flooding.
As a result of the apocalypse, Tokyo was destroyed and is rendered uninhabitable due to suffering extreme damage.