Tomoharu Natsume survived a horrible plane crash but Misao, his close friend, did not and became a ghost that continued to be attached to him. Three years later, he moved out to a place rented by his brother to live on his own and attend Raku High since his mother remarried. On his first day in his new house, a mysterious girl called Shuri turns up and gives him a silver briefcase to look after on behalf of his brother who lives abroad. Soon after, Tomoharu and his best friend, a ghost named Misao Minakami, are attacked by various factions who all seek the 'Asura Machina' and 'Extractor'.

After the events of the previous evening Tomo and Misao learn about the Royal Dark Society from Shuri. Later he runs into Takatsuki whilst visiting his new landlord and learns that she was the one who broke into his house in search of the briefcase. However, soon her father arrives and things get awkward for Tomo when he realises that he was one of the people responsible for the destruction of his house. Tomo is then confronted by the First Student Council President, Saeki Reishirou, who was also one of the people who raided his home.

Having been captured by Saeki, Takatsuki is put on trial and sentenced to death for her involvement with Tomo. Meanwhile, Tomo rushes to retrieve the Asura Machina and save her from the First Student Council. However, when he finds the trunk empty he must rely on Shuri's help to save the day.

The science club head to Lake Tobi to investigate reports of a mysterious creature terrorising the area. Unbeknownst to them two fellow students, Kurasawa Rikka (the Second Student Council President) and Mahiwa are also ine the area searching for the creature. It soon emerges that the monster is in fact a familiar that was abandoned by Mahiwa and has gone berserk. Armed with this knowledge the science club set out to reunite the two and stop the creature's rampage.

When Shuri is injured during a fight with an Ausura machina she her personality completely changes and she thinks her name is Kurosaki Yukari. This prompts Tomo to investigate her life but soon both Tomo and Shuri are attacked by a murderer-doll only to be saved by Takatsuki.

Shuri arranges to trade the real stabilizer with Susugihara for something very important to her. However, with Tomo still too ill to use Kurogane there is no-one to fight her when the trade goes badly wrong and as such they are forced to flee.

Now that Kurogane has absorbed the stabiliser, people can see Misao, but Tomo is worried that she won't be able to hide her incorporeal nature from those around her. Meanwhile, Haruna and Susugihara explore a strange set of ruins in search of the Caster Machina. These recent events prompt the group to look back on the tragic plane crash which started them in motion, not only for Misao and Tomo, but for Shuri and Susugihara as well.

With a large creature mysteriously attacking demons, Takatsuki is forced by her family to move in with Tomo so that he can protect her. At the same time Shuri arrives with a young demon named Ania, who Tomo also has to protect. However, Ania is a 'Luck-Eater' and causes misfortune to befall Tomo and his friends. Things get even more complicated when it turns out that Ania's sister, Kristina maybe involved with the demon hunts.

When an Asura Crying appears during Reishirou's attempt to stop the culprit behind the demon hunts he explains how Tomo is also in danger of becoming one and orders him to leave the matter alone. However, with Ania desperate to find out what has happened to her sister and Tomo sworn to protect her it isn't long before he is face to face with the Asura Crying.

The Second years are preparing for a class trip to Hawaii. Meanwhile, Tomo and Misao attend a party hosted by Reishirou in memory of the anniversary of Aine's death. The party also features a very unusual performance competition in which everyone from Rikka to Takatsuki takes part and which Tomo and Misao end up winning.

While, Shuri and Reishirou are enjoying their Second Year trip to Hawaii, Tomo accidentally stumbles across a Plug-In for the Asura Machina. However, Kagakagari also wants the device and he attacks Tomo and the others in order to retrieve it. As such Tomo is forced to break his promise to Takatsuki and use Kurogane to fend him off.

Kagakagari has taken a plane full of people hostage and offers to exchange their lives for the Igniter. However, the exchange soon turns violent putting the lives of the hostages at risk. Tomo must then attempt a very dangerous plan using Kurogane in order to save everyone that he cares about, but will it be enough?