This story is sort of a re-vamping of the original ending of Devilman. The story begins a few years after the events of the last film, and Japan has become a chaotic world, where demons run loose and attack people in the open. A "demon alert center" has been formed, and humans are encouraged to report any demons on site. Some neighborhood citizens go out on demon patrols, both to combat them and so that other humans don't suspect them as being demons themselves. Akira has formed the "Devilman Army", which is comprised of Mico and other half-demons like himself. The story begins with Mico and Yumi being attacked in the open by a demon named Zouvo, and saved by Akira.

Meanwhile, Ryo appears on a television news program with footage of Akira's transformation into Devilman. With the secret out, Akira high tails it to the Makimura home in fear that Miki might be in danger. Miki arrives to her home to find that her parents have gone out demon hunting, and her brother Taro is home alone. She retires to her room, unaware of the group of men that has quietly broken into her home. Taro is watching the television while the footage of Akira turning is broadcast, and before he can tell Miki about Akira being a demon, he is shot in the head with a crossbow by one of the intruders. Miki, hearing a noise ventures downstairs to find Taro's head still stuck to the wall, and his bloody body below it. As she backs away, she too is killed.

Akira arrives at the Makimura home to find the townspeople have burned the home, and are dancing around a long pole with Miki's head at the top. The shock of the scene quickly gives way to the anger and the transformation to Devilman. The next scene is of Akira still half demon, standing in a mass of blood and bodies. Amidst the carnage of the dead townspeople, He gingerly picks up Miki's head and cradles it on his shoulder. His eyes fill with tears as he lets out his rage. As Akira cries in anguish, Satan is watching from above.

Akira is seen in solitude sitting beside Miki's head, remembering the past. Mico standing silently in the shadows watching him, is startled by Yumi, entering to tell Akira that one of the Devilman army has been ambushed by a group of demons led by Saylos. Akira rises to take care of business, and feels a shift. As he realizes something isn't right, hordes of demons crash through the windows and surround them. Saylos, the leader of the group offers Akira the chance to join them. Akira's earlier suspicion plays true, before he has a chance to do anything he goes into spasms as he feels the separation take place, resulting in the leveling of the building they are all in. When the smoke clears, the demon army see a figure emerge from the debris. They are shocked to see it is Amon, the God of War and the demon who was possessed by Akira to become Devilman. Amon quickly gets rid of every demon in Saylos' army, eats Yumi, and then goes after Saylos. Amon and Saylos battle it out, which leaves Saylos with a crater for a stomach. Amon then sets his sights on Satan.

Amon confronts Satan, and attempts to take his rage at being possessed by Akira on Satan. Psycho Genie thwarts his attempt. Satan informs Amon that Akira is still alive, and we are set up for the final showdown. Amon and Devilman face off in wildly aggressive battle. Amon gets an early advantage, and beats Devilman to the point of death. While Devilman lays bleeding, he envisions Miki and is able to finally lay her ghost to rest. This gives him the strength he needs to continue fighting Amon, and this time defeats Amon. We next see Akira falling from the sky and crashing to the ground, the force of his fall leaving a rather large crater in the shape of Devilman.

In the final sequence, Akira has buried Miki's head, and is kneeling by the grave when he feels a presence. He raises his head to find Ryo standing a few feet away. Akira quietly rises and moves towards him, neither making a sound. The two former friends stare blankly at each other for a moment, and then silently Akira walks away and turns his back on Ryo agknowledging that he now knows what Satan's plan was all along.