Only a few hours prior, Akira Sengoku was enjoying himself with his classmates aboard their flight returning to Japan from a school trip in Guam. Now, he finds himself isolated in a jungle following the plane's mysterious crash. As he searches for survivors, his environment grows increasingly suspicious when he encounters various animal species he has never seen before. Eventually, he locates two survivors—his classmate Shirou Mariya and cabin attendant Kanako Oomori—who are being attacked by a two-meter tall bird! After barely escaping with their lives, Shirou uses his computer to determine their precise location and clarify the nature of the strange creatures they have encountered. His discovery exceeds anything they anticipated: they have crashed on a Pacific island that should not exist, inhabited by animals that supposedly went extinct millions of years ago. Eden no Ori recounts the struggles of Akira and the other survivors on an island all too eager to see them disappear. With predators lurking around every corner, Akira and his friends must employ all their wits to survive and unravel the mysteries of the island's origin.