Just a few hours ago, Akira Sengoku was having fun with his classmates on their flight back to Japan from a school trip in Guam. Now, he finds himself all alone in a jungle after the plane mysteriously crashed. While searching for survivors, his surroundings become increasingly suspicious as he stumbles across various animal species he has never seen before. Finally, he manages to find two survivors—his classmate Shirou Mariya and cabin attendant Kanako Oomori—being attacked by a two-meter tall bird!

After barely managing to escape with their lives, Shirou uses his computer to pinpoint their exact location and shed some light on the strange creatures that they have encountered. What he discovers is beyond anything they expected—they have crashed on an island in the Pacific that should not exist, inhabited by animals that supposedly went extinct millions of years ago.

Eden no Ori tells the story of Akira and the other survivors' struggles on an island all too eager to see them disappear. With predators lurking around every corner, Akira and his friends must use all their wits to survive and unravel the mysteries of the island's origin.