Pita Ten surrounds a boy named Higuchi Kotarou, in his last year of elementary school. He's a hard-working but fairly average boy, who studies a lot to try and raise his grades even though that still only makes them borderline. His mother died when he was young (which he blames himself for) and his father's hardly ever home, so understandably he's always felt a little empty inside. His best friends are Ayanokouji Takashi (Ten-chan) and Uematsu Koboshi. Koboshi has had a crush on him ever since she's known him. They don't make it clear whether he's completely oblivious to this or if he's just pretending not to know in order to try and keep things from getting complicated.

One day a really weird girl (Misha) appears next door and immediately starts acting very friendly, a friendliness which is unwelcomed by Kotarou, who has put walls up around him to try and protect himself from getting hurt. Despite Kotarou's obvious discomfort, Misha does everything she can to keep Kotarou happy and safe. However, Misha is an idiot and although she means well she often does more harm than good. Sometimes she does well though and even Kotarou can't shield himself from such unconditional affection. But why does she act this way towards him? Who is she? Where did she come from? And why Kotarou?

Add another into the mix. A kind, gentle girl by the name of Shia who's background is also unknown and was originally suspected to be not quite normal, and share's Misha's interest in Kotarou (although not romantically). She says she's 'searching for something'. What's she looking for?