Demons have now become commonplace around the kingdom of Midland, which has fallen into chaos. The swordsman Guts still cannot stay in one place for long due to his demonic brand. He could always manage to protect himself when he was alone, but now he has the added challenge of protecting former Commander Casca, a shell of her former self who neither remembers nor trusts him. They never have a moment's rest with the constant threat of demons, and they need a place where Casca will be safe till they find a way to heal her. Their elf ally, Puck, tells of the mystical land of Elfhelm, which is supposed to be a safe haven from the demons that ravage the lands. Tired and with only a vague hope, they struggle on to find a place to live—and they still need to find those responsible for the madness they are forced to endure.

Set in a different series of events, this story does not follow the previous Appleseed movie canon (despite being directed by the same director of the previous movies); it is an alternate story to their beginnings. Briareos is already a cyborg and did not become separated from Deunan to be later reunited in Olympus to join ESWAT. Appleseed Alpha depicts the early days of Deunan Knute and Briareos in the 22nd century, as they embark on a journey throughout dystopic ruins of New York in search of the city of Olympus. They are hired by Two Horns, the warlord of the ruined city, to eliminate bipedal combat machines. During the fight, they encounter Iris and Olson, both on a mission. Deunan and Briareos befriend them and decide to join their mission. Iris is tasked with preventing the malevolent cyborg Talos from capturing a secret weapon humans were building. Talos uses Iris to activate the gigantic war machine. (Source: Wikipedia)

The Band of the Hawk and their enigmatic leader Griffith continue winning battle after battle as their prestige throughout the kingdom of Midland grows. But their latest task is one that has seen failure from everyone who has attempted it: the subjugation of the impenetrable fortress of Doldrey. But with members like Guts—the captain of the Hawks' raiders who can easily fell 100 men with his gigantic sword—such tasks prove to be trivial. However, in the aftermath of the battle, Guts decides to leave the Hawks in order to pursue his own dream and bids farewell to his companions, despite Griffith's attempts to make him stay. This single event causes Griffith to lose his composure, and leads him to make a decision that will alter his and the Hawks' fates forever.

The Band of the Hawk has dwindled in the year since Guts left them on his journey to forge his own destiny. Unaware of their fate, Guts returns to the Hawks—now being led by his former ally Casca—after a rumor about them passes his way. Once the saviors of the kingdom of Midland, the Band of the Hawk are now hunted as they desperately fight for their lives while plotting to free their leader, Griffith, after he was imprisoned for committing treason. But the man they save is far from the Griffith they remember. Griffith is a shell of his former charismatic self after a year of continuous, horrific torture. No longer able to walk, speak, or even hold a sword, he has nothing but the small, strange trinket, the Crimson Behelit, that will not leave him. The entire Band of the Hawk want to rise to greatness once more, but how much are they willing to sacrifice to return to their past glory? It doesn't seem possible, but when Griffith's heart darkens and a solar eclipse blackens the sky, the Behelit offers a choice that will leave the Band of the Hawk with a blood-soaked fate that will haunt them for the rest of their days.