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.

When the Granites nab Phryne during the Star Festival ambush, the temple authorities retaliate with an attack on the secret village in hopes of recovering the priestess.

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.

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.