Depois da última Onda, Naofumi, Raphtalia, Filo e Rishia se dedicam a restaurar o vilarejo de Lurolona antes da próxima Onda. Quando alguns monstros surgem, Naofumi percebe que a contagem regressiva parou.

Naofumi derrota diversos familars para proteger a cidade em que está e acaba encontrando uma mulher misteriosa. Mais tarde, em uma reunião com autoridades de diversas nações, essa mulher surge mais uma vez.

The Spirit Tortoise begins its march once more, appearing at the border of the kingdom bearing its name. Naofumi volunteers to lure away its familiars while the army tries to bring it to the mountains. The Spirit Tortoise’s familiar, Ost, fights alongside the humans…

Naofumi acaba visitando o interior do Espírito da Tartaruga e reencontra rostos conhecidos.

Naofumi is met by L’Arc, Glass, and Therese. They’re after the person who broke the Spirit Tortoise’s seal and is controlling it. L’Arc proposes teaming up again…

Fitoria appears when the Spirit Tortoise revives, and with her help, Naofumi attempts to destroy its heart and cut off its head at the same time. L’Arc arrives as well, but all of them are helpless before Kyo’s overwhelming power.

Naofumi wakes up in a strange prison to find him and his party at level 1, and Filo missing. They start to raise their levels in order to escape, but things quickly turn against them when a dangerous monster suddenly appears…

Naofumi’s party heads for the Dragon Hourglass of Mikakage, in order to get to Sikul, the country that summoned Kizuna. Along the way, he sells rare healing items to make a hefty profit. He hears a rumor about a genius mage…

Naofumis party is teleported to Sikul, where Kizuna introduces the Vassal Weapon Hero, Ethnobalt. He soys he can use a piece of Raphtalia's hair and Naofumis blood as a catalyst that can create a shikigami to find her. He creates the shikigami, and they find.

Raphtalia is imprisoned in a Raybul Kingdom prison. She’s wary of L’Arc’s team, who is also imprisoned there, but asks them for help in escaping. Glass is weakened by the draining power of the prison. Raphtalia has a plan to escape, but…

Naofumi's party is overjoyed to be reunited with Raphtalia. Kizuna criticizes Glass for invading another world. Glass and L'Arc swear they won't fight Naofumi anymore, and instead find another way to solve their problem. Meanwhile, Kyo's plot proceeds.

The Wave appears before its scheduled time. Kizuna's group is teleported to it while Naofumi and his party head for Kyo's lab on Ethnobalt's ship. There, they see the true depths of Kyo's wickedness...

Raphtalia recalls having to buy clothing for her smaller self. Kizuna remembers being alone for so long. Rishia remembers Ost trying to give advice.