One by one, the people she met at Guriel and her attendants are swallowed up by the tornado, leaving Alisha all by herself. As she wanders, she comes upon an ancient ruin and finds a mural depicting the “Shepherd,” who will save the world from calamity. But she is attacked by a huge swarm of insects. Alisha barely gets away alive and as though guided by the crest of the Shepherd, arrives in the celestial capital. Just around that time, Sorey, a human youth who resides in Elysium, Home of the Seraphim, and Mikleo, a young Seraph, have also come to the ruins.

Sorey decides to take Alisha, the young girl he meets in the ruins, to Izuchi. Mikleo doesn’t care for the idea of taking a human, but Sorey just cannot ignore someone in need. When they reach Izuchi, Alisha passionately calls out to the seraphim to help her. But her pleas seem to go unheard. It is because the seraphim believe that humans will bring calamity to their land. Although she had believed in the seraphim, a forlorn Alisha concludes that the Celestial Record was a legend and nothing more.

After Alisha leaves, Sorey fears that the mysterious man that appeared in Elysium is after her. So Sorey, accompanied by Mikleo, head for Ladylake, the water capital where the Sacred Blade Festival that Alisha mentioned is being held. Upon arriving in the capital, and seeing the human world for the first time, Sorey cannot hide his amazement at the people and scenery. Thanks to a young girl named Rose who comes to his rescue, he is able to enter the city. But the capital is teeming with Malevolence which causes Mikeo to grow physically weak. During that time, Sorey sees the man who was after Alisha.

In order to save the people from the hellion that appears in Ladylake, Sorey extracts the Sacred Blade of the Lady of the Lake which would make him a Shepherd. He brings down the hellion, but Sorey himself collapses and regains consciousness later. Donning the legendary Shepherd’s attire given to him by Alisha, Sorey goes into town. The streets are lined with banners bearing the Shepherd’s crest and he realizes how much hope the people place on the Shepherd. Later, Sorey becomes the vessel of the Lady of the Lake and gains the ability to perceive Malevolence. And sensing Malevolence, he searches for its source in the aqueduct.

Velvet – a woman who is in prison. Devouring monsters called “daemons,” she has lived in confinement for several years. Velvet has only one purpose in life. To get revenge against the man who leads the Abbey, an organization of exorcists who possess the power to battle daemons. To bring down the man they call their savior, Artorius Collbrande. One day, Artorius’ former partner, a Malak known as Seres, appears before Velvet to try to help her escape.

Velvet escapes from the prison tower with the help of a young daemon named Rokurou. The only way to access the island prison is by ship, so she and Seres head for the harbor. But Oscar, the praetor exorcist who has been ordered by Artorius to subdue Velvet, is already there. Velvet takes him on. Oscar believes in the natural law of the world that Artorius espouses. But Velvet cannot forgive such a world that was made possible by the sacrifice of her younger brother. Completely at odds with each other, the fighting continues...when suddenly, a dragon appears.

Sorey listens to Lailah explain about the Shepherd's true mission when a dragon appears. It goes away without attacking Sorey, but the townspeople who see this are overcome with gratitude, and even Barltow himself invites Sorey to his mansion. On the way there, Sorey see miasma from the Malevolence rising up among the people. He resolves to pursue the dragon in order to stop the Malevolence before it can spread in Ladylake. Meanwhile, Mikleo begins to ponder what he must do to inspire Sorey who is now a Shepherd.

Mikleo goes to the Galahad Ruins in search of the legendary Divine Artifact that can suppress evil spirits. Meanwhile, after parting ways with Alisha who is headed for Marlind, Sorey goes to Rayfalke Spiritcrest which appears in dragon folklore. There, he encounters a young seraph named Edna being attacked by a hellion. Sorey and Lailah confront the hellion, but the Malevolence is too strong and they cannot deliver a decisive blow. Suddenly, another seraph named Zaveid appears and makes quick work of the hellion, declaring that killing hellions is his style. When Sorey objects, the seraph cryptically counters with ”Maybe some are saved by killing them.”

Alisha’s party and the medical unit find the bridge leading to Marlind collapsed due to the heavy rains, and start searching for a detour. Meanwhile, Sorey continues his journey and reveals to Edna the seraph that he is going to Rolance, which is rumored to have many ancient ruins where dragons were deified as gods. Sorey’s earnest faith in the writings in the Celestial Records exasperates Edna, but she opts to tag along. Later, Lailah asks Sorey, “What does ‘purify’ mean to you?” This causes Sorey to reflect on how he must confront future hellions. About that time, Mikleo, armed with a Divine Artifact, heads for Griftlet Bridge where a maelstrom of clouds swirls overhead.

Sorey pursues the elusive Drake to Marlind and reunites with Mikleo who has acquired a Divine Artifact in the form of a bow. Entering into a Sub Lord pact, they armatize and successfully purify the Drake with an arrow. Later, they go to help with the reconstruction and set about purifying the town’s water. Sorey accompanies Alisha to disperse emergency supplies that have arrived from Ladylake and encounters Rose, the Sparrowfeathers merchant who helped him when he first arrived in Ladylake. Her group has also brought supplies from Ladylake.

Sorey and the others leave Rohan the seraph and Atakk the Normin seraph to watch over Marlind, and head for Glaivend Basin at the border of Hyland and Rolance, where Bartlow is attempting to incite a war. Sorey warns Alisha that if war has begun, he will side with neither Hyland nor Rolance. But as a Shepherd, he wants to stop the fighting. Sorey and company reach Glaivend, only to find a battlefield teeming with Malevolence. Alisha sets out to convince Hyland’s General Landon to stop the fighting, but Sorey tells her “I am going to do what I can.”

War inevitably breaks out between the Kingdom of Hyland and the Rolance Empire. Just at Bartlow had planned, Alisha is stabbed by a soldier from her own kingdom. Meanwhile, an immense mass of Malevolence appears before Sorey and company on the main battlefield. It is none other than Heldalf, the Lord of Calamity. Sorey sees the real Heldalf in the center of the Malevolence and declares that he will “purify” him. Even as countless hellions summoned by Heldalf charge at him, Sorey has faith in his power and the power of his friends, and continues to fight.