Sword destroys a Horror that has been killing people, causing considerable destruction in the process. Meanwhile, Sophie consults the fortune teller "Moon Wizard" to locate her missing brother, but he turns into a Horror. She only just escapes with her life and then Sword arrives on his motorcycle and destroys it. Sword then takes her to his favorite diner and Makai headquarters for a meal. It appears that they both seek "El Dorado". He promises to protect her although he also asks her to be bait for a Horror who has been hunting red-haired women. The strategy works and Sword destroys the Horror, however again causing considerable destruction.
Following massive damage to a city bridge during Sword's battle with a Horror, Luke fires his special gun into the sky, causing it to rain and wiping the memories of everyone in the vicinity. Luke meets Sword in the diner, berating him for his irresponsible methods. Later Hardy, a former world champion runner who is now crippled in a wheelchair, allows himself to be possessed so he is able to run again. Finding Hardy gone, his girlfriend Enith asks Sword for help to find him. Meanwhile Hardy is now a Horror and has developed a hunger for human flesh. Hardy returns home and attempts to kill Enith but Sword intercepts him, however Hardy is too fast and it takes the combined efforts of Sword and Luke to destroy him. Again, Luke uses his rain-making gun to wipe the events from the memories of everyone in the vicinity including Enith who resumes her search for the missing Hardy.
Sword's old acquaintance, Makai Alchemist Gina, is in town to investigate an up and coming gangster named Damian Stewart because of his apparent access to the city’s information network. Sword is disinterested until Gina mentions Damian may have information on "El Dorado". Meanwhile Gang bosses gather to plot against Damian, but he because he already knows about the meeting, he ambushes them. Damian then takes a surviving gang boss and feeds him to his massive computer system which is possessed by a Horror. Sword agrees to cooperate with Gina to discover Damian's secret. She infiltrates one of Damian's exclusive pool parties and obtains a sample of his DNA to breach the security system, giving Sword an opportunity to investigate. Sword finds the possessed computer which tries to kill him, but he manages to destroy it instead. Although Sword spares Damian's life, the surviving gangsters take their revenge on him.
Sophie's roommate tells her that Father Ripley went missing and Sophie goes to find out more about his disappearance. He apparently lived with his sister Marie in a renovated church. At the residence she finds Marie living alone, looking frail and sickly. Suddenly Sword arrives and presents Marie with a bunch of flowers for the loss of her brother. Sophie and Marie share their stories, and become friendly, but that evening, when the talk turns to her brother Father Ripley, Marie has a flashback to when her brother treated her badly and imprisoned her in the basement. Marie suddenly changes and becomes violent and, fearing for her life, Sophie tries to escape. She finds herself locked in the basement which is filled with instruments of torture. Marie bursts into the basement and transforms into a Horror, but Sword arrives and a battle ensues. Although Sophie tries to help and is almost killed, but is saved by Sword's motorcycle. She again pleads with Sword to help her find her brother.
Surprisingly, Gina asks Sword to marry her. Her plan is to infiltrate the house of a successful woman called Viola, who apparently has a magical ring that is able to control Horrors. She made her fortune helping wealthy families deal with their difficult children, but some seem to have disappeared. Gina, Sword and Sophie go her mansion as the Brown family. While sword keeps Violet occupied, in bed, Gina and Sophie explore the mansion and find signs of Demons. Viola finds them both, and Gina realizes that the woman has been consumed by the Horror herself. A battle ensues, which is only ended when Sword arrives and kills the Horror Viola. Later, in the diner, Sophie again presses sword to help her find "El Dorado".
Sophie continues to press Sword to help her find "El Dorado" and her brother, and tracks him to the Chinese restaurant where he lives and works. Meanwhile Luke and Sword receive instructions to investigate a movie theater where people seem to disappear. Luke goes alone, leaving Sword to "babysit" Sophie, however he finds nothing amiss. Sophie accesses online chat rooms and finds some references to a particular seat in the theater, L13. Luke watches a movie in that seat, and has a vision of being with his family in the past. At the end of the movie, Luke has disappeared. Sword visits the theater and Zaruba detects that the entire theater is the Horror. Sword plunges his sword into the seat, opening a pathway into Luke’s vision where Luke is caught up in the memories of his past and Sword calls him back. Luke recovers his senses and blasts the Horror with his magic pistols and Sword joins the battle. After they destroy the Horror, Sword tells Luke that it was due to help from Sophie that Sword found him.
Pawn, a scout for Eldorado, meets professional woman, Melia Wild, but before they can discuss business, Pawn turns into a Horror and devours her. Elsewhere the mysterious white-haired Knight appears in the city looking for Sophie. Pawn later appears at the Katrina Home, offering Sister a free holiday to El Dorado for the children. Meanwhile Sophie finds some references to El Dorado in the chat rooms, but the users have disappeared, including a seven-member team. She manages to trace them to a local shop. When Sword and Luke go to the shop, they find the missing people alive but unconscious and call Feilong for backup. Meanwhile Pawn appears at the school early, eager to take the children. Sister resists and valiantly fights back while Sophie helps the children escape and desperately calls Sword for help. Suddenly the Knight appears and kills Pawn, but then also kills Sister as well in front of a horrified Sophie. Knight tells Sophie that his master, the King of El Dorado, has summoned her, but at that moment, Sword and Luke arrive and confront Knight.
Sword protects Sophie while Luke confronts Knight and an all-out battle ensues between them. Luke recalls when he was a trainee and the Silver Knight his teacher, before he became the Dark Knight. The fight continues, but Dark Knight is too strong and impales Luke with his Naginata. Sword then attacks Dark Knight and they both turn into their Makai Knight forms and continue the battle. Meanwhile Feilong's people set up a magical barrier around the knights to protect the city and prepare to evacuate Sophie. As Meifong takes Sophie to a safe underground shelter, they are intercepted by a Horror, but Meifong manages to defeat it with a magic talisman. The battle between the knights takes on epic proportions with entire buildings being destroyed in the process. Eventually they confront each other without weapons, but as Sword gains the upper hand, Dark Knight departs, vowing to return.
In the aftermath of the battle with the Dark Knight, Sister's funeral takes place and Luke is alive but badly injured, both physically and emotionally. Sword is given instructions in the diner to head west with Sophie in search of El Dorado and its king and to meet up with additional Makai Alchemists at San Del Rios. Sword and Sophie travel through the countryside beyond the city. They come across a wounded deer and Sophie insists on stopping and helping it and she realizes how much she misses Sister. Meanwhile in El Dorado, Dark Knight is criticized for his failure to capture Sophie while they await Sword’s impending arrival.
Emergency services deal with the casualties from the battle. Meifang patches up Luke and reminds him of his duty to destroy Horrors, their number increasing since some protective barriers have been destroyed. He experiences the effort made by humans to selflessly help others. Again Luke thinks back to his time as a child training with his parents to fight Horrors and how his father killed his mother in a quest for greater power. He recalls his dying mother's words that power is not an end in itself, but to be used to protect others and realizes that he must follow Sword to El Dorado to help him confront its king.
Sword and Sophie stop in a western town, Sun Dell Dios, while they wait for reinforcements. However the town is run by a vigilante group led by the sheriff Alfil. The townspeople try to take Sword into custody because they believe he kidnapped Sophie, while the waitress, Natalia, grabs Sophie and Alfil drives them out of town. When Natalia tries to sedate Sophie, she causes the car to crash. Back in town, Sword runs from the townspeople, unwilling to harm humans, and is eventually rescued by the arrival of Gina. Meanwhile Alfil reveals that he is a Horror and prepares to take Sophie captive, but she shoots him before he changes, and gains a reprieve until Sword arrives. While Sword fights the Horror Alfil, Bishop appears and prepares to take Sophie whom he calls princess, but again Gina comes to the rescue. Realizing the usefulness of the town has ended, Bishop reduces it to dust, however Gina had taken the precaution of placing a barrier around the townspeople so they were saved. As Sword, Gina and Sophie prepare to continue their journey, Zaruba compliments Sophie on her resourcefulness.
A stranger, looking for his friend, stays the night in a remote, run-down roadside motel, but a Horror violently kills him. Meanwhile Sword, Sophie and Gina drive through another ruined and rough western town. They arrive at the same motel where they decide to stay after days of sleeping rough. While there, Sophie meets a teenage boy, George, the lonely son of the owner Matthew and his wife. As Gina and Sophie take a bath, a liquid-based Horror attacks them, but Gina drives it off. Later, Matthew's wife discovers that her husband made a pact with the Horror to ensure the family's financial survival. Matthew wishes to return to Russell City and become a success, but instead, the Horror engulfs him and then attacks his wife. She is saved by Sword who, together with Gina, attacks and destroys the Horror. Before moving on, Gina rewrites wife and son's memories to eliminate their experience, believing instead that a tornado caused the destruction and Matthew's death.
Gina suggests that they visit Ferre Salé Dessimo, a Makai Alchemist village in the Land of Guidance, to get more information about El Dorado. They arrive at a modest settlement built on islands of woven reeds on a lake in the mountains, where an elder tells them that El Dorado has become a problem. Gina, Sword and Sophie travel to the Land of Guidance and enter the temple that only appears on a full moon. Gina undergoes the trial, defeating wolves and a monster then receives a ruby colored gem. She is also told of the powerful ring possessed by the king of El Dorado, a place which lies beyond El Sanvados to the southwest. As they set off, Gina gives the gem to Sophie.
Luke arrives in a town after being sent by the Land of Guidance and visits an old man and his granddaughter Stella with a Makai Alchemist symbol on their door. Stella, an avid researcher of the occult, tells him the legend of a Demon Sealer who sealed a demon nearby many years ago. Apparently the seal has weakened and the demon is about to awaken with the impending full moon. They take him to the place where a statue of the Demon Sealer once stood and with Luke's help, locate a sea cave where the demon was sealed. Luke identifies it as a Knight that became a Horror. The next night, Luke goes to the cave to prevent the Horror from reappearing and Stella follows him. The powerful Horror awakes and Luke tries to fight him with all the weapons at his disposal, including the spirits of those the demon defeated in the past and he manages to destroy it. As he leaves, Luke wipes their memories of the previous night's events.
Five bus-loads of young people, the chosen ones, head into El Dorado hoping to fulfill their dreams. Meanwhile a Horror, Bezel, has infiltrated El Dorado and walks the streets looking for King, consuming humans along the way, however his presence is detected by Bishop. One of the chosen ones, a young girl accepts a free invitation to an exclusive party, but she find that it's an trap to provide food for the resident Horrors. Bezel interrupts their feast and kills them all, although he is observed remotely by Bishop and Queen. Bezel approaches King's golden tower where he challenges Queen. He splits into multiple clones, however Queen is prepared and easily disposes of them and she defeats Bezel. He survives and just manages to escape with his life, only to be destroyed moments later by Knight.
Sword, Gina and Sophie arrive at a seaside town, but Sophie is angry at Sword for eating her chocolate without permission. During the day, Sword saves a boy named Pedro from some thugs whom he blames for the death of his girlfriend Monica. Pedro ask for Sword's help but Sword refuses as he recalls the death of his own sister in an explosion the research facility of Signa Slam Tech and the fruitlessness of revenge. Pedro again gets beaten up, and Sword again rescues him, chasing off the bully. As they prepare to leave the town, Sword gives Sophie a present of chocolate and her anger dissipates.
As Sword, Gina and Sophie approach El Sanvados, they are confronted by a battalion of Horror bikers. Sword attacks them, sending Gina and Sophie ahead by another route in the car. However Bishop sets up a Horror Barrier darkening the sky, and follows Gina and Sophie with a wave of flying Horrors. They are almost caught, but Luke arrives just in time, destroying the Horrors and breaking the barrier. Suddenly a new monster emerges from below the ground and captures Sophie just as Sword arrives on his motorcycle. Sword rescues Sophie and then Zaruba carries her away to safety on the motorcycle. Sophie is distressed at the trouble that she has caused her companions, but Zaruba tells her to keep moving forward. When they are caught by Knight, Zaruba crashes the motorcycle into Knight, sacrificing himself. Sword, Gina and Luke catch up with Sophie and Luke absorbs the remaining power of the Madou ring in preparation for a showdown between the Makai Knights. However, after testing Sword's powers, Knight withdraws leaving Sophie and the others to mourn the loss of Zaruba.
Gina separates from the crew to restock her wares, but the remaining members finally enter El Dorado. Sophie wants to find her brother as soon as possible and thinks finding King may be the fastest way. In her search on ELDO NET, she meets a clown...
Sword, Luke, and Sophie prepare to raid the GarEden Corporation only to find out they are too late, the true El Dorado has reached completion. They rush in, knowing full well that their enemies are waiting for them within. Waiting for Sophie.
Sophie finally reunites with her brother, but something is wrong. In his mind, she's still a 10 year old girl and the things he says doesn't match what she knows. At the same time, Sword also meets someone from the past. An illusion? Or something else?
Sophie is heartbroken her brother is already a Horror. Martin finds out the truth about all the work he has been doing for Sophie. While Sword and the others rush to Sophie's side, Sophie searches for her unstable brother to finish things herself.
Sophie discovers that she was the trigger that King had prepared for her brother Martin, who carried no inner darkness within him. Now that King has taken over Martin's body, he moves forward and releases ELDO NET into the world.
Sword and Sophie go back into ELDO NET, determined to destroy the storage container that holds all the souls abducted by the system. Lizzy helps them on the inside, while Luke and Gina protect the duo from the forces on the outside.
King has been destroyed, but a few loose ends still need tying up. Per Sword's request, Luke erases Sophie's memory so that she can return to her normal life. Her days are peaceful, but in the back of her mind, Sophie knows she has lost something.