Amanda suspects a connection between Joseph, the mysterious man witnessed around Gerd, and the Blassreiter that fought with Gerd. She subsequently starts her own investigation. Meanwhile, the XAT witness a sudden change in the condition of the victims that were exposed to the Amalgam's attack. The victims start to show signs of transforming into an Amalgam themselves.

One of the XAT members, Herman, has been seeking the Amalgam that appeared at the race circuit. He finds out that the very man he is looking for is Joseph. He searches Joseph out and manages to corner him....

Joseph barely escapes from the XAT but is seriously injured. He collapses from exhaustion and his wounds. When he recovers consciousness, he finds himself sheltered in a warehouse containing waste disposal.

Gerd is tormented by the fact that he has become a beast, and as a result goes wild. He tries to fight against Joseph but is immediately contradicted. Joseph explains that he need not die if he is able to maintain his humanity. Meanwhile, Herman devises a plan to use Malek to stop Gerd.

Malek is devastated by Gerd's death. Joseph is worried about Malek and tries to stay close, remaining within the city. However, a security camera captures his transformation, and subsequently XAT learns his true identity.

Malek's despair drives him beyond the bounds of reason. He transforms right in plain view of his bullies and starts taking his revenge. XAT agents arrive on the scene, but Malek attacks them as well. Joseph tries to persuade Malek but fails. XAT enforcements arrive and start preparing for a full-force attack on Malek.

In an effort to save Malek, Amanda sets out on a search with Herman. Meanwhile, in an abandoned church, Joseph's long-standing target of pursuit appears.

Joseph and Malek are taken into custody in a XAT laboratory. Amanda goes against orders to transfer them to a different government agency and starts to analyze Joseph's data with the aid of Herman and a XAT researcher. There, she comes across a top-secret report code-named "Blassreiter."

XAT agents begin to fall ill, one after another. Then one day, in response to a massive emergence of Amalgams in the city, the agents themselves start turning into Amalgams. A fierce battle breaks out within the XAT ranks who have turned into Amalgams and those who have not, when at last, Joseph regains consciousness.

Al and Brad start showing subtle signs of Amalgamation, but Amanda and Herman are unaffected. Amidst the inferno of ex-XAT agent Amalgams running amok, Al and Brad pledge their allegiance as XAT agents to protect Amanda and Herman until they are safely out of XAT grounds.

Amanda takes the injured Joseph to a dilapidated church. There, Amanda learns of Joseph's past and of his parents who died to protect him. His parents were what ordinary citizens called "Outsiders," a class of people considered inferior. Joseph was brought up by a priest who continuously reasoned with him that however harsh the world is, there must be some meaning to his life. However, reality as an Outsider was far harsher on young Joseph than anyone could ever imagine...

Joseph is now 15 years old. He meets a young doctor who is engaged in support activities for Outsiders such as Joseph. Joseph is touched by the doctor's belief that normal citizens and Outsiders are both creations of god and thus should be treated equally. Joseph begins assisting the young doctor's activities when a group of mindless citizens attacks the doctor and injures him. At the hospital where the doctor is taken in, Joseph meets a woman named Sasha who is the doctor's friend.

Joseph and Amanda are caught and taken to the headquarters of Zwölf, a mysterious institution that meddles in forbidden science. Among its members called Apocalypse Knights are people whom Amanda knows well, and this deeply disturbs her. The Apocalypse Knights manipulate specially developed ultra-weapons and easily take down the horde of Amalgams that had previously given XAT such a hard time. Amanda is more enraged rather than stunned.

Hermann, now a Demoniac converted by Beatrice, infiltrates the Zwölf castle in order to see Amanda. Meanwhile, Wolf leads a Demoniac force to attack a Luftwaffe air base in order to draw attention of the Apocalypse Knights. Demoniac-manned Eurofighter Typhoons were used to intercept the Knights with Beatrice coming close from behind. Hermann later turns to an Amalgam and escapes with a Paladin motorbike, killing Zwölf defense personnel in his wake.

The Apocalypse Knights take on the Demoniac Eurofighter Typhoons and Beatrice, while Amanda confronts Hermann in his Blassreiter form and helps him realize what he is supposed to be fighting for. He and Amanda arrive near the Luftwaffe airbase, now damaged by a bomb to kill off the Amalgams and prevent them from attacking nearby towns and cities. The two of them face off against Wolf and his Amalgam cadre.

Amanda and Hermann engage Wolf and his Amalgam cadre until Joseph enters the scene in his upgraded Blassreiter form, making him attack both friend and foe. Wolf retreats due to casualties, but not before luring Joseph to attack Amanda and Hermann. At the United Nations, the ambassadors have been concerned about the inability of German security forces to handle the Amalgams and agrees to send in UN peacekeepers to eliminate the Amalgams after being told of the elimination of XAT and the capture of the Luftwaffe base. Victor communicated with surviving members of the German government after the country has fallen to a near state of anarchy. Amanda encounters a young Blassreiter named Snow while trying to locate Hermann.

Snow confronts Joseph and gets him out of his berserk state. Hermann and Amanda confront Wolf and the remaining Amalgam cadre at the former besieged XAT Headquarters before an Amalgam Al attacks the two surviving XAT officers. But seeing his name of Amanda's Paladin brings Al back to his senses as he attacks Wolf. With Amanda and Hermann teaming up, Wolf had been defeated and was killed for good. Al killed himself afterwards with his sniper pointing at his chin because he doesn't feel that coming back to life was normal.

A horde of 30,000 Demoniacs head towards Zwölf under the command of Xargin with Beatrice following him. Zwölf sends Joseph out to delay his advance towards Zwölf headquarters, wounding Beatrice in the ensuing fight between them and was about to end her life when Xargin interfered despite the modifications given to him on Victor's orders. Amanda and Hermann infiltrate the Zwölf castle to rescue Malek in the midst of the fight.

Armed Zwölf defense personnel were mobilized to ward off the Demoniac invasion on Victor's orders. Victor heads down to the server room to secure computer data during the invasion when Xargin encounters him in the room and kills him for good. Amanda and Hermann escape from Zwölf HQ with the wounded Joseph and Malek in tow in the midst of the Demoniac fight against the surviving armed Zwölf forces in the castle HQ.

Amanda and Hermann take refuge in a small compound managed by Amanda's aunt, a nun who took charge of an unconscious Malek. Sasha hands Amanda the Isis data, which contains the information needed to defeat Xargin's Demoniac forces after deleting the data at the Zwölf castle since Xargin was able to penetrate it. Malek, after realizing that he could do good with his Blassreiter powers, revives from his coma and attacks Beatrice to give Hermann time to fatally wound her. Hermann dies in the fight, being glad that Malek accepts him as an older brother. Meanwhile, United States Air Force B-2 Spirit bombers are being deployed as part of the UN's mission to eliminate the Demoniacs in German soil.

Meifong, Sasha and Shido work together once more to defeat United States Air Force B-2 Spirit bombers and F-35A fighters from conducting a bombing sweep of Germany to clear out Demoniacs. Xargin confronts Malek and the two engage each other in their Blassreiter forms. Shido conducts suicide by destroying his Sword Rider unit, defeating the last F-35As and the launched missiles with help from Sasha and her Bow Rider. Joseph, now recovered, confronts Xargin and swallows the Isis pill as the two men engage one another in Blassreiter form after getting a tired Malek out of Xargin's way. Sasha and Meifong were busy preventing a missile orbital bombardment on German soil from space as a last means of preventing Demoniacs from crossing German land borders to other European countries.

Meifong and Sasha are the only remaining Zwölf personnel to counter the ICBMs being fired on towards Germany. Joseph and Xargin engage each other in Blassreiter forms with Gerd and Hermann assisting the former by using their powers on his body. Sasha dies when her Bow Rider explodes from overheating while Meifong is killed after engaging a spacecraft over the Earth. Joseph, after the Isis pill is used, dies with its particles killing Xargin and his Demoniacs by making them solid for good. 5 years after the events of Blassreiter, Germany was able to rebuild from scratch and the federal government reformed XAT with Amanda as a leading officer. The reformed XAT was given a new mandate to protect people who have the ability to turn to Blassreiters. Malek is indoctrinated into XAT due to his abilities as a XAT special agent.