Having overcome countless trials (without much difficulty), Yogiri and Tomochika finally managed to reunite with their classmates in the capital. But between the efforts of Ayaka, a synthetic classmate who swore revenge against her fellow students, the meddling of Sion, a Sage determined to cull the weak and produce a new superbeing from their class of candidates, and the revival of the Dark God Mana, the majority of the class — not to mention the entire capital — were ultimately wiped out.

Somehow, amid the chaos, the unlikely pair were able to draw Sion out and acquire their first concrete clue about how to get home: they will need a number of Philosopher's Stones, powerful artifacts carried within the bodies of the Sages. After taking one from Sion and finding another dropped into their laps by Risley, the only surviving clone of the Sage Lain, who they killed some time earlier, the two highschoolers set off in search of a third energy source, leaving a trail of ruins behind them.