Boukyaku no Cradle

From MangaHelpers:

The world is in a tense political situation, and one country has instituted a new mandatory education program for all children fifteen and up. It's a half-year program that puts the children through military training. Kazuki has traveled to an installation on Yurikago ("Cradle") Island for his half-year of training along with many other boys. Kazuki has no special physical talent, but he has a remarkably good memory. His closest friend in the training, Sai, is top-notch at everything and not particularly liked by some in their class.

One day, their relatively ordinary life in training comes to an abrupt end. Kazuki awakes to find the island facility in ruins. He has no idea how much time has passed, or what has happened. Soon he meets up with Sai and a strange little girl with a cat, and they begin to try to figure out their situation. What has happened to the island, and to their country? [tethysdust]