The story of Chaos Legion is a gothic opera which begins November 791 A.S. (Anno Satanis). The protagonist, Sieg Wahrheit (from the German words for "victory" and "truth"), is a Knight of the Dark Glyphs who is on a quest to find his former friend Victor Delacroix ("champion of the cross"), who has stolen the forbidden book Apocrypha Of Yzarc ('crazy' spelt backwards), and to stop him from releasing the spirit Azrail who will destroy the three planes of existence (the Nether World, the Middle World, and the Celestial World). In the beginning, Delacroix feels that Sieg was responsible for the death of his lover,Siela Riviere, and is intent on bringing Sieg into a pure pandemonium that Delacroix himself has prepared as retribution not only for the sins of Sieg alone, but for the sins of the whole world. Delacroix refers to this armageddon as the "Purification of the World," whereupon he plans to use relentless hordes of hideous monsters to cleanse the world of sinners.
During his quest, Sieg encounters a member of "The Maidens Of The Silver" fighting a monster alone after other Maidens are killed. With Sieg's help Arcia Rinslett, the sole survivor, manages to escape death. At first, Arcia mentions that the Maidens of the Silver were in tough pursuit of Delacroix; thus, when she learns that Sieg is also searching for the same person, she decides to tag along. Later, it is revealed that Arcia has held a grudge against Delacroix for the murder of her brother.
Sieg never tells Arcia why he pursues Delacroix even though he does say the two knew each other. Because of this lack of trust, Arcia briefly loses her faith in Sieg and sets off to find Delacroix alone. Sieg eventually catches up and subsequently teams up with her once more after he consoles her. Sieg and Arcia meet Delacroix several times, each time to have a little more of Delacroix's plan revealed. Soon Sieg and Arcia meet Delacroix in the Hall of Chaos, the place where Azrail is sealed. Delacroix decides to punish Sieg first by killing Arcia with her own gun, since it seems that Arcia is close to Sieg. The murder fails, unbeknownst to Sieg who lashes out and attacks Delacroix because he believes Arcia to be dead. After subduing Delacroix, Sieg learns that Arcia survives the shot, only to find that Delacroix is not fully defeated. Surrounded in black aura, Delacroix attacks Sieg once again, but Arcia steps in between Sieg and Delacroix, with her arms outstretched. Instead of killing her, Delacroix regains his right mind, and a flashback takes place which reveals the truth of the past.
Several years before, Sieg, Delacroix, and Siela were ordered by the Order of St. Overia to reseal the demon Azrail. In reality, the Order planned to use Azrail's power for world dominance, but realized that Azrail was too powerful to contain. The demon resisted and decided that instead of being banished once more, it would possess a human: Siela. Delacroix tried to protect Siela but was possessed instead. In his uncontrollable rampage, he almost killed Sieg, but Siela withheld the mortal wound, and Delacroix drove his sword straight through her chest. When he came back to his senses, he believed Sieg had committed the murder. Siela's dying words to Sieg beforehand were: "Take care of Delacroix..." This is the reason why Sieg can't directly kill his friend.
Back in the present time, Delacroix decides to end his own life, much to Sieg's dismay. The only way to break Azrail's seal is to kill the person who last created the seal or perform a secret ritual sacrifice described in the forbidden book Apocrypha Of Yzarc. Delacroix breaks the seal by sacrificing himself. Azrail is then released and fights Sieg not only in its own demonic form but also respawned in the form of Dark Siela to intimidate him. However, Sieg prevails. After all the chaos, Sieg mourns the loss of his two best friends, but Arcia cheers him up and relieves him.