Tomoharu is a normal high school student... except for the fact that he is never alone. Haunted by the ghost of his dead childhood friend, he moves into a new residence at the beginning of the school year. Life turns out to be a little more difficult than expected, though, when his house is overrun by various female occult users. To make things even worse he is pulled into an epic struggle to protect a mysterious trunk, that is presently hidden in the house.
Whilst being forced to clean the school pool Tomo and the rest of the Science Club stumble across an underground cavern which leads them to the Rakuroa Ruins. Here Tomo sees a strange vision of an alternate world. However, before he can learn more the group is attacked by Castas Machina guarding the ruins and Touru has to show up to save them.
Tomo is growing increasingly concerned about Misao and asks Shuri and Touru to locate his brother, Naotaka. In exchange Tomo must persuade the reclusive Science Club president Tokiya Kagayaki to return to school. However, this is not as easy as it first sounds so Tomo takes Misao and Takatsuki along to help. Tomo also learns that Touru and Tokiya have a very tragic connection to Kurogane.
Tomo, Takatsuki, Misao, An and Higuchi are all enjoying a working vacation at the beach but it isn't long before Tomo manages to upset Misao. Meanwhile, Shuri and Ania are investigating the ruins on a nearby island. However, it seems that Kagakagari and Kristina are also interested in them, as is Kyomu Satomi and the First Student Council.
Tomo and the others are apparently saved by Tomo's brother, Naotaka and then taken in by Kagakagari and Kristina. Kagakagari reveals that the ruins are the remnants of an Asura Machina testing ground and that they may contain a way to free Burial Dolls like Kotori and Misao. However, before they can retrieve the device Kyomu arrives and tries to use Ania as a hostage.
Following a mishap with some industrial strength glue whilst practicing for the three-legged race, Tomo and Takatsuki end up stuck together for the rest of the day. As if protecting each other's modesty and organising sleeping arrangements weren't trouble enough, Takatsuki's family is currently under threat from a rival group of demons who are out to assassinate them.
After receiving a cryptic warning from his brother, Tomo and the others come under attack from a mysterious woman and are forced into a trap set by Hiwako Torishima. The group are then saved by a powerful Asura Machina and Tomo makes a serious of shocking discovery's about his brother, Misao and the Asura Machina themselves.
Despite having been arrested by Haruna, along with Tomo and the others, Ania is kidnapped by Hiwako's masked henchwoman. Hiwako then offers to trade Ania for Tomo and the group decides it is the perfect opportunity to ambush her, with Susugihara's help. However, things go badly wrong when it is revealed that Hiwako, Touru and Tokiya have been working together behind the scenes and even the appearance of Naotaka is not enough to halt their plans.
Following Hagane's attack Tomo awakes to find himself all alone in the First World with no idea of how to get back. He soon encounters the 'Witch of Rakurowa High School', a strange Daughter and very strange versions of the people he knows. However, after a chance encounter with Tokiya's sister Aki he is reunited with Takatsuki. He also learns more about the Superstring Gravity Reactor accident that started everything.
Having been reunited with Ania, Tomo learns more about the effects that the Superstring Gravity Reactor accident is having on the First World and Ania's involvement with it. Later when a large group of Daughters attacks the school Aki and Ania are forced to use their demonic powers to protect those they care about and Tomo learns that in this world he has powers of his own.
Tomo finally gets to meet with the real Naotaka and learns that there is a way to save the First World even without Hagane. However, the plan is extremely dangerous and there is no guarantee that both Tomo and Misao won't be killed in the process. In the end the plan is a success but unfortunately Takatsuki ends up getting hurt and there is nothing Tomo can do.
Now back in the Second World Tomo and the others discover that they have 10 days until Tokiya can set his plan in motion. Tomo also discovers that he has inadvertently entered a contract with Takatsuki and that they now have a Daughter, Persephone. As if that wasn't enough Tomo is then appointed as the new President of the Third Student Council. Unfortunately, there is no time to deal with all of these new events as Tokiya has a found a way to accelerate his plan and Tomo must once again try to save the world.
Tokiya has managed to open the gate to the Third World and the Second World has begun to vanish at an alarming rate. As such Tomo and the others must gain access to the Central Vortex in order to confront Tokiya and save the world. However, with Tokiya in control of not only Hagane but Hisui, Bismuth and Rhodonite as well that may not be as easy as it sounds.
Natsume Tomoharu and his friends goes to save the world. Tokiya Kagayaki wants to keep the Igniter so he could have a third world that has Aki, his lover. After Tomoharu defeated Tokiya, the Igniter seems to respond to Tomoharu's wish and closed the gate to the third world. After that, Ania Fortuna told Tomoharu that she completed the Splitter. So then she asked if Himazasa and Misao Minakami wanted to become human again and they did. After that everything became normal and all demons became humans. Everything from the First world disappeared including the Asura Machinas. Ania and Vivian returned to their normal sizes.
