Iriya no Sora, UFO no Natsu

Iriya no Sora, UFO no Natsu is a story revolving around a secret war that has been going on below the public's eye since 1947 and a group of people involved in the war, either directly or indirectly. The main protagonist is a young high school student named Naoyuki Asaba who, on the last day of summer break, sneaks into the school at night to swim in secret. However, upon arrival at the pool, he meets the mysterious Kana Iriya, who is there for the same reason. However, she doesn't know how to swim, so Naoyuki offers to teach her how to swim. During this private lesson, a group of people show up in search of Kana and take her back to the nearby air force base where she is staying.

The next day, Naoyuki is surprised to find that Kana joins his class as the new term begins. Eventually, both of them take a liking to each other and Naoyuki even gets her to join the school newspaper club. Little does Naoyuki know that Kana is in fact an expert fighter pilot engaged in a war between humans and aliens that has been going on since the Kenneth Arnold incident on June 24, 1947. The whole world's fate rests in the hands of Kana Iriya and if she can ultimately hold off the invasion in the final battle.

[From Wikipedia]

This is the DS version of the first 2 light novels in the series.