While Clain is on his way home from the junk market, he saves a mystifying girl from peril—but she disappears from his life as quickly as she entered it, leaving only a mysterious pendant behind.

When Clain examines Phryne’s pendant, a life-like girl named Nessa appears. When her curiosity and odd behavior causes trouble, Clain is forced to leave her in the city—but he can’t shake a new feeling that something is amiss.

Enri flies her hostages to her brother in the village of the Granites, home to a faction of the Lost Millenium. There Clain learns there’s more than meets the eye inside the Fractale system.

A glitch in the Granites’ getaway ship has them stumped—but Clain uses his hacking skills to reveal a mischievous doppel that can’t resist a game of hide-and-seek!

The Granites' land their ship out of range of the Fractale system to make repairs. Clain and Phryne take in an eye-opening view of the effects of Fractale's failing structures after they meet a lone antique collector.

After they crash their ship, Clain and an ill Nessa find themselves in the extravagant city of Xanadu under the care of deceptively friendly doppels.

The high priest holds Phryne and the wounded Clain in an underground base. A Nessa look-alike shows Clain how much the temple cherishes Phryne. Meanwhile, Sunda recruits the other Lost Millenium factions for a rescue mission.

After the Granites lift Clain, Phryne and Nessa safely from the rubble of the destroyed lab, the factions of the Lost Millennium face the fateful decision to unite for their best shot to bring Fractale down--or surrender.

The battle between the Lost Millenium and the temple's forces rages on. Phryne reaches the Archpriestess, but will her pleas to end the war and let Fractale fade out fall on deaf ears?

Clain is helpless behind a clear wall as Barrot details Phryne's role in the system, but the priest's demented rant is cut short. As the temple begins to collapse and Nessa starts to fade, the future of Fractale--and all of mankind--lies in Phryne's hands.