Naofumi follows the slave merchant to his store, where he looks for a partner to act as his sword. But all he has the money to buy is a diseased demi-human girl named Raphtalia, whom he then forces into an incredibly harsh battle.

The Wave is gone, but Naofumi's relief is short-lived as Motoyasu challenges him to a duel in the middle of the celebratory banquet held in Melromarc Castle. Motoyasu insists that owning a slave is unbecoming for a hero and that Naofumi free Raphtalia at once.

After Aultcray reluctantly offers Naofumi a paltry reward, he heads to the slave merchant to redo the slave crest as per Raphtalia's wishes. He also buys a monster egg there, which hatches a few days later and gives him a new party member. Meanwhile, Myne shows up in Lute Village, where they're staying.

In the Eastern village, Naofumi meets a girl named Melty. She instantly becomes friends with Filo and then requests to accompany the party on their journey. It seems she got separated from her guards. They travel together for a while, but when they reach the capital, they find...

The Pope holds in his hands the ultimate weapon, which possesses the properties of all four cardinal weapons. Faced with its attack skill, "Judgment," and its powerful defensive force field, Naofumi and gang are rendered helpless. As the crisis worsens, Motoyasu, who is now in line to be punished as a "fake" hero, makes a surprising decision.

Naofumi and gang stay on the attack despite being trapped in the Pope's Great Cathedral, but its sacred subspace nullifies his Curse Shield, leaving them one step short. Naofumi turns to another, newly unlocked Curse Shield, but the dragon's wrath threatens to swallow his mind whole.

After being unable to for so long, Naofumi finally gets to upgrade his party's classes. He then takes part in a meeting of the Four Cardinal Heroes, held under the guise of a celebratory banquet. There, he learns of the existence of a bonus stage, with increased XP earnings. Meanwhile, Raphtalia gets into a fight at the party.

On the ship to Cal Mira, Naofumi once again runs into L'arc, who keeps throwing him off. However, the strange man's friendly nature shines through, and Naofumi quickly takes a liking to him. After having a fun time grinding levels and a lively meal, Naofumi feels happy and fulfilled for the first time in this world.

Melromarc brings a large fleet to fight the Wave out at sea. While the queen takes charge and leads the operation well, the other three heroes prove useless yet again, leaving Naofumi to do it all alone. Later, he gets help from L'arc and Therese to fend off the monsters, but then...

It turns out that Glass, like L'arc, is also a hero from other world. Naofumi barely fights off their combo attacks and then corners Glass in a one-on-one battle, but is then faced with an all-important question: does he truly wish to protect this world?

Mysterious monsters appear as Naofumi is preparing for the next Wave. At the same time they show up, the Wave countdown stops. The Queen summons the Four Cardinal Heroes, and tells them that the Spirit Tortoise has revived.

The Spirit Tortoise’s head was cut off, but Ost, its familiar, is still alive. It could revive at any moment. The allied armies need to get back into fighting shape, and fast. Naofumi makes the risky move of heading onto the Tortoise’s back with only a small group, and tries to find its true weak spot.

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…

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…

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.