In a world covered by an endless sea of sand, there sails an island known as the Mud Whale. In its interior lies an ancient town, where the majority of its inhabitants are said to be "Marked," a double-edged trait that grants them supernatural abilities at the cost of an untimely death. Chakuro is the village archivist; young and curious, he spends his time documenting the discovery of newfound islands. But each one is like the rest—abandoned save for the remnants of those who lived there long ago. For the first time in six months, another island crosses the horizon, so Chakuro and his friends join the scouting group. During the expedition, they find vestiges of an archaic civilization. And inside one of its crumbling remains, Chakuro discovers a girl who will change his destiny and the world inside the Mud Whale as he knows it. [Written by MAL Rewrite]

While walking home, Mikiya Kokutou comes across a familiar sight: Shiki Ryougi standing by a railing amidst the falling snow, just as when he first met her four years ago. While the two talk of their past and shared experiences, Mikiya realizes that something is strange about Shiki; rather, this is not the woman he has come to know, but an entirely different entity that dwells within Shiki's body...

After losing a bet, Keiichi, Mion, Rena, Satoko and Rika parade around the town in costumes. When they come to a fork in the road, they decide to go to Yagouchi, a nearby abandoned village. Once there Keichii and Rena learn the mystery of a strange haunted quarry as they debate whether or not to check it out.

In 20xx, a civil war broke out in a small country in Asia in spite of the dispatch of UN forces. But a picture taken by accident in the battlefield accelerates the peace process: a photograph of a flag, which became the symbol of peace. However, just before the peace agreement is finalized, the flag is stolen by an armed extremist group in order to obstruct the truce. To rescue the flag, the UN sends the Special Development Command (SDC, which is armed with the High Agility Versatile Weapon Carrier (HAVWC)), along with an embedded photojournalist to record their activities. That photojournalist is Saeko Shirasu—the young camerawoman who took the picture of the flag. (Source: ANN)