College student Iwatani Naofumi is reading a book titled "The Records of the Four Cardinal Weapons" in the library when he is suddenly summoned to another world and told he has to save the world as the Shield Hero, one of the Four Cardinal Heroes. And one morning, he finds all his money and equipment gone.
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.
Naofumi has obtained a whole load of abilities and skills, and his teamwork with Raphtalia is reaching perfection, too. To prepare for the incoming Wave, he upgrades their equipment and heads to the dragon hourglass to find out exactly when it will arrive. But there, he runs into Motoyasu and the other heroes once again.
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.
The mysterious girl that showed up out of nowhere was actually Filo. She's a filolial queen with an advanced transformation ability, and she can even take human form thanks to it. However, her clothes get ripped every time she transforms, meaning Naofumi has to get her some magic clothes if he doesn't want to go broke. The party leaves on a new adventure to gather the materials required.
After hearing of a village that's in immediate need of herbicide, Naofumi and his party head there to do business. The village has been overrun by plants that have turned into monsters, and its residents were forced to abandon it. These plants can even take root in humans, and apparently Motoyasu is the one who released them into the wild.
After hearing of a village in the East that's being ravaged by an epidemic, Naofumi and his party head there to deliver medicine. The epidemic was caused by the corpse of a dragon that had been killed a month before and left there to rot. Naofumi's party accepts a job request to clean the corpse and head to the mountains where it lies.
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...
After refusing to hear Melty out, Naofumi switches to planning for the next Wave. When a bunch of young soldiers ask to join his party, he agrees, but on a certain condition. At the same time, he also tries to upgrade Raphtalia's class after she hits the level cap, but all he receives is harassment.
Naofumi faces another Wave, this time in a remote village. With the help of the soldiers who volunteered to join him, he's able to secure the safety of the villagers, but the Wave shows no signs of letting up. He heads to fight with the other heroes, only to find a giant ghost ship floating in the sky.
A mysterious woman showed up out of nowhere and destroyed the second Soul Eater in a single blow. She then proclaimed the start of the "true battle of the wave" and blew away the other three heroes when they attacked her. With Naofumi's party proving ineffective as well, he decided to use the Rage Shield one more time.
Naofumi foils the attempt to take Melty's life and fights off the royal knights, but he's then framed for abducting Melty and killing several knights, so the party is forced to go on the run. With security tightened and checkpoints everywhere, the party receives a further blow that only makes things even worse.
Due to Myne recklessly starting a forest fire, Naofumi and his party are forced to flee to a village at the base of the mountain. However, it won't be easy to break through the knights' net. Melty suggests going to a noble she knows for help, and it just so happens that Raphtalia's past is linked to his domain.
Raphtalia corners Idol with vengeance in her eyes, her bloodthirsty blade reaching for his throat. Naofumi's words bring her back to her senses momentarily, but when Idol attacks her once again...
As Naofumi and his party try to get the weakened kids to safety, Tyrant attacks them. Once Naofumi realizes that he's actually after Filo, he hatches a plan to lure him outside the city, but they can't even put a scratch on its massive body.
Fitoria tells Naofumi that she'll kill all Four Cardinal Heroes if they don't get back on the same page. She even takes Melty hostage, but Naofumi continues to refuse. Understanding where he's coming from, Fitoria instead proposes a one-on-one duel with Filo.
Naofumi decides to go straight up to the checkpost in order to talk it out with the other heroes. But there, he finds the one guy least likely to listen to him, Motoyasu, who attacks Naofumi without bothering to listen to what he has to say. Why could Motoyasu be so intent on killing Naofumi, more than ever before?
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 Naofumi survives thanks to Mirelia's help, she comes to visit him and tells him the truth behind the summoning of the heroes and the discrimination against the Shield Hero. She also promises to clear his name, and holds a trial for Aultcray and Myne's crimes.
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?
