Born from a cocoon in the village of Old Home, a young Haibane—a being with a halo and small gray wings—awakens to a world she does not understand without memories of her past. Named Rakka for the dream of falling she had while inside the cocoon, she soon becomes accustomed to life in the strange town. However, there are strict rules for the Haibane, such as being forbidden to leave the village or go near the walls surrounding it. These, along with mysterious disappearances of their kind on their "Day of Flight," begin to unsettle Rakka and the others since they know almost nothing about their own kind. Haibane Renmei tells not only Rakka's story but also of those around her, as they live their lives with no memories of the past while trying to break free from their former pain and ultimately find salvation.

Akihiro is a teenaged boy with fantasies. He's about to have date with his girlfriend Miyuki when he finds a strange carpet on his way home. Home, a pretty and over-energetic girl named Malon appears from the carpet. She tells Akihiro about the world of Phantasia and wants to live with Akihiro. But even if Akihiro loves pretty girls, he becomes angry with Malon's magical powers and drives her away. The maniac wizard, Roll, who wants to kill Malon, doesn't help at all.

In the aftermath of the most devastating conflict mankind had ever experienced, the tiny island of Shikotan became part of the Sakhalin Oblast... and on the unhealed border in this remote corner of the world, friendship among children from two different countries timidly blossomed, striving to overcome language barriers and the waves of history. Inspired by true events. On August 15th, they told us we had lost the war. At that time, we did not really understand. Then one day, everything changed. Many soldiers, wearing uniforms we had never seen before, arrived on the island. That was the day I met Tanya.

Ryuuichi Kaizu, intelligent, ambitious, and dedicated, but at the same time cunning and immoral young student receives present from girl Emi Naito, who comes from wealthy family. Realizing that being in relationship with her can help him reach his goals, he decides to make her his, without her even being aware she is just another woman he is using.