A young girl dreams of falling endlessly, only to awaken inside a giant cocoon. Upon her hatching, mysterious beings known as Haibane seek to ease her transition into this strange new world.
Rakka begins to explore her surroundings: an abandoned dormitory called Old Home. As she grows stronger, her new friends slowly introduce her to the rules and regulations of a Haibane's second-hand existence.
Hikari and Rakka journey to the temple of the Haibane-Renmei, where Rakka's new life is issued to her in the form of a notebook. Later, an outburst from the Young Feathers leads to a quest for pancakes.
Rakka continues her search for the perfect job by hauling trash and fixing broken timepieces with Kana, an opportunity which affords her a rare look at the city walls from a lofty vantage.
A day spent working at the library leads Rakka to search for the long lost secret behind the beginning of the world. Meanwhile, out in the street, Reki is harassed by a cruel male Haibane.
With winter approaching, Rakka begins looking for a room of her very own. Kuu is quick to offer assistance, but her flickering halo and sudden disappearance raises concern among the other Haibane.
Rakka - still mourning the loss of Kuu - is distraught to discover black spots spreading across her wings. Ashamed, she obsessively cuts off the diseased feathers until Reki puts an end to her self-mutilation.
Rakka's fragile emotional state and blackening wings drive the young Haibane to follow a crow deep into the Western Woods, where she discovers the secrets of her cocoon dream.
After Togas rescue Rakka from the well, she is drawn to the city walls by the phantom sound of Kuu's voice. Her decision to touch the forbidden barriers leads to an encounter with the Communicator.
Bits and pieces of Reki's tragic past are revealed in a flashback, and Rakka visits the Communicator to return his staff and accept her unusual punishment for touching the wall.
Rakka learns more about Reki's past during a visit to Abandoned Factory, the co-ed living quarters for wayward Haibane. Later, a disturbing revelation from the Communicator causes Rakka to fear the worst for her friend.
The Passing of the Year Festival has arrived, and time is running out for Reki. Making peace with the dwellers of Abandoned Factory may be her only hope for finding the forgiveness she desperately seeks.
Reki steals away in the night, but Rakka tracks her down, determined to save her tortured friend. An outburst of hurtful words from Reki brings tears to Rakka eyes, but will they be enough to make her give up hope?
