Like any huge city, there is darkness beneath the blinding lights and towering buildings of Russel City. Makai Horrors dwell within that darkness and hunt humans. Tonight as well, a girl that is searching for something late at night is being hunted.

The morning after a crazy night, a strange rain begins to fall upon the bewildered construction men, washing away their memories of the entire. A single man stands watch with an umbrella overhead. His name is Luke, a Makai Alchemist.

The beautiful Gina tries to infiltrate her way to the top floor of a building owned by a big-time gang boss, but finds out it's a bit more than she can handle. She meets up and asks Sword for help, sweetening the deal with a little bait of El Dorado.

Sophie continues the search for any clues that may lead her to her brother, Martin. Since the word "El Dorado" was the only thing her brother left behind, she desperately tries to hunt down the elusive Sword in order to gather more information.

What is El Dorado? Sophie pesters Sword for an answer and meets Gina for the first time. Perfect timing, as it seems Gina needs both a husband and a child for her next treasure hunt. Gina takes Sophie along to show her just what it is that they do.

Sophie sticks with Sword, hoping for some new leads on El Dorado. Luke finds out about her and voices his disapproval to Sword. All the while, it seems there is a movie theater where couples go and sometimes one of them disappears by the end credits.

A sudden increase of missing persons cases are plaguing Russel City. All of the victims are young adults heavily involved with the internet. A message about El Dorado is left behind by one of the victims and the crew begins their frantic search.

Sword and Luke chase after the knight of darkness, who was once the powerful Silver Makai Knight. Fei Long and Meifang support them and protect Sophie from Knight's grasp as Sword and Knight battle it out and the city falls to shambles.

Russel City works on recovering from the mysterious disaster that hit their city. The diner sends Sword and Sophie out west, to find El Dorado and take down Knight before he has a chance to make a second attack. Sophie travels with Sword in a daze.

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 Sword 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.

Sword, Gina, Luke and Sophie finally arrive at El Dorado, a glittering island city separated from poor people wishing to gain entry. Luke creates a memory-removing rain shower over the border guards enabling him, Sword and Sophie to enter while Gina travels to the Land of Guidance to replenish her weaponry. Following his orders form the Watchdog Centre, Sword plans to find out the real identity of King. They explore the city where everything appears to be made by the GarEden Corporation. Sophie enters the amazing Eldo Net virtual world and finds the happiness there is very superficial, but then she receives a suspicious invitation to find out more. Suspecting a trap, Sword, Luke and Sophie meet the citizen who sent the message who reveals that the apparent utopia is run by Horrors who use it as a feeding ground. Suddenly, his hideout is attacked by assault Horrors, so the citizen transfers his data to Sophie's cell phone which enables her to access the secure network and track the approaching Horrors. They also discover her brother Martin Hennes is the programmer involved with El Dorado and receive a message apparently sent by Sword. Later, they help the citizen escape, but are left with even more unanswered questions.

Bishop sets in motion plans to capture Sophie, an apparent obsession of King. Sophie researches the GarEden Corporation online and finds it merged 10 years ago with Signa Slam, a company that Sword recalls was involved in a Horrors attack which resulted in his sister's death. Inside El Dorado, Sword, Luke and Sophie find that Makai plants are taking over, devouring the human population as they go but find a lone human survivor. They encounter Queen who uses the carnivorous plants to attack them while the survivor turns into the Makai Alchemist Stanley who abducts Sophie. She manages to escape into the complex, where she finds a door marked Martin Hennes. On touching the control panel, the door opens, and she finds what appears to be her brother’s office, a diary and many fake letters to him apparently written by her. She is caught again by Stanley, but Sword and Luke find her and the battle continues. However, Sword is unable to stop Bishop who throws Sophie into a vat of liquid at the center of the birthplace of Eldorado and she loses consciousness. She appears to awake back at home where she sees Sword and his sister Lizzy, and meets her brother Martin.

In her unconscious dream, Martin proudly shows Sophie the virtual city that is El Dorado where people address him as King although he says he is only the system administrator. Meanwhile, Sword tries to determine how he can be with his dead sister Lizzy. She offers him information about El Dorado while Luke carries his unconscious body to safety. Lizzy explains to Sword that the people in El Dorado are the souls of people who have died and been captured. She says that the ancient Horror King infiltrated Cygnusram-Tech and completed the theory of Eldo Net, however his plan was discovered by Makai Knights and although the facility was destroyed, he survived. Suddenly Lizzy and Sword are discovered, and the population change into robots and attack them. Lizzy then asks Sword to save Sophie and destroy El Dorado. Meanwhile, Sophie realizes that Martin is unaware that thousands of humans have been sacrificed to fuel the ancient Horror King’s version of utopia, and the ring that Martin wears enables him to control them subconsciously. Sophie attacks Martin and he eventually sees the tortured bodies of the sacrificed humans. Tearfully, Sophie threatens to kill her brother.

In a flashback to when Sophie and Martin were orphans, Martin promises to protect Sophie and create a world free of difficulties. Back in the present, Queen berates Bishop for failing to kill Sword while he observes Sophie attempting to kill her brother because of the lives he needlessly sacrificed for her happiness. Frightened and confused Martin escapes into the complex. Meanwhile, Sword, Luke and Gina look for a way to shut down El Dorado, however Queen moves to intercept them using her Carnivorous Plants and turning citizens into Horrors. Leaving the others to fight Queen, Sword goes looking for Sophie. Martin recalls three years earlier when he was first approached by Queen from the GarEden Corporation who gave him a Madou Ring, and he begins to realize that he has been duped and used to create the fiction that is El Dorado. Outside, with Gina's help using a sniper rifle, Luke finally manages to shoot Queen. Inside, Martin finds Sophie, but the Madou Ring consumes him and turns him into a Horror, displaying his wretched face on its chest.

Bishop remotely watches as the scene between King and Sophie unfolds and thinks back to when he recruited the naive Martin Hennes. Sword finds Sophie and they watch as King causes El Dorado to be bathed in a red light. Sword and Sophie are suddenly surrounded by hoards of demonic creatures, but they are rescued by Zaruba on a reconstructed motorcycle. Sword and Sophie then lead the surviving citizens out of El Dorado. With Sword, Luke and Gina reunited, they realize that King's plan was to use Sophie to take over her brother Martin via the Madou Ring Bishop gave him. A message from Lizzy is broadcast on all TV screens, warning that as King consumes the souls within El Dorado he will grow stronger. She also tells them that Sophie has administrator access to The Eldo Net storage unit that houses the souls. Zaruba convinces the despondent Sophie to join the others with the ruby colored gem given to her by Gina. Suddenly Knight and Queen attack the group, but Luke and Gina stay to fight the two 'blades' of King, while Sword rides back into El Dorado with Sophie.

Sword bursts back into El Dorado with Sophie on his motorcycle and they meet Lizzy, but then become surrounded by King's robots. Sword remains to fight them while Lizzy take Sophie to attempt to deactivate the Eldo Net system. Meanwhile Luke and Gina engage in all-out individual battles with Knight and Queen. Sword is sucked into the digital void that is King and fights against a myriad of digital constructs, but eventually, by combining his Makai Knight form with Zaruba, cuts down King. Sophie struggles to destroy the Eldo Net storage unit, and when one of her tears falls on the ruby gem, she again sees Martin who gives her the password “everything is for my sister”. She uses the password to delete the data and Eldo Net begins to disappear, but as Sword exits the King's void, he is intercepted by Knight in his Makai form.

Confronted by Knight in his Makai form, Sword changes into Golden Knight, and they engage in a titanic battle using their motorcycles, swords and fists, until Sword finally destroys Knight. Meanwhile outside, Sophie wants to ensure that Sword is safe, but Luke fires a rain-making bullet that erases her memories. A year later, Sophie has settled in back at the orphanage, although she feels that something is missing from her life. However, after seeing blood when she cuts her finger, she recalls the ruby gem pendant and with that, her memories come flooding back. She rushes to the diner where she finds Gina who tells her that Sword is fine. Sophie then asks her how to become a Makai Alchemist, wanting to prevent the same events occurring again. Later Bishop enjoys his freedom from control by King, and Sophie finally meets Sword again, emerging from the kitchen in the diner.