Shining Ark's story is about a boy named Freed who meets an angel-like girl named Panis.
Freed lives in Arcadia, a faraway island natural beauty with ancient ruins. One day Freed sees a mysterious girl with one black wing. Panis has an innocent personality and the miraculous power to gather animals when she sings. Amazed, the islanders begin to call Panis an angel. However, when the moon shines the sky turns red and a gigantic thing is drawn towards her.