>>909664
You have to pay attention to the plot, what's going on and be able to formulate what it all means by yourself by the end. In short, humanity wrecked the planet and instead of trying to fix shit, they decided to fight over what was left and created "new weapons" in order to do so.
Japan's so happened to be some uncontrollable nanite thing and when the world realised what it was capable of (as we see by the end of the series with Chise being some world ending spaceship), the world decides to invade Japan. It also doesn't help that it acts out on its own and starts destroying foreign cities.
That said, the manga does it way better than the anime, but it's the same for the most part. However, there's a lot going on behind the scenes and you are expected to piece things together yourself. Both in the anime and the manga.