The Innocence of the Heart is the last hope we have. The darkness is rising.

It's been two years since Allen Walker has been sentenced by the Exorcists as a prisoner and betrayer, and many things have changed. The Noah's have fled back to Edo, discontinuing their search for Innocence to destroy it as they find out that the Millennium Earl has disappeared. With an unknown leader, a Noah who is taking the place of the Earl until he returns, takes control of a dark army of Akuma growing stronger, the where-abouts of Millennium Earl seemed to disappear when the last encounter he had with Exorcist had persisted for far over a month. No one was found. Road Kamelot, who was often seen with the Earl seems to be hiding something from the others and assures them that he will return as she closely watches the new Dark Prophet closely. While the Noah Clan continues to build onto his dream of a new world under Darkness, each of the clan members begin tracking down innocence one by one by murdering Exorcists.

The Black Order is dying, Exorcists running short quickly. Three of the generals have passed, and the Order must choose new Exorcists to take their places. Retrieving the innocence from fallen exorcists seems to get harder as each death with every exorcist seems to become more violent and destructive. Allen Walker has been released from his chains after signs of Neah within him have become neutral. The Exorcists continue to hide secrets from him though, and watch him closely to make sure that the moment he snaps once more, he is left behind bars, or even worse. After a long time of observation, something strange occurred; Neah had split from Allen. With new, young Exorcists coming in, The clergymen and generals are getting worried that they may not be able to train fast enough before the hours of darkness arrive. Time is running short for the Black Order, and they still need to collect 67 pieces of Innocence, and are yet to know where the heart is.

The Black Order headquarters located in Europe was destroyed by the Millennium Earl several years before, leaving the original exorcists (including all the canons) to retreat to the Asian Branch. While doing so, some stayed behind to help rebuild the European branch once more. After it was rebuilt, some returned to it, but it was mostly left to welcome new exorcists who joined. Many of the exorcists who moved to the Chinese Branch decided to stay there. While this was taking place, the Millennium Earl had also traveled with his minions to the other countries, destroying all other headquarters, leaving only the Europe Branch and the Asian Branch left. Many exorcists have fallen, and the generals are growing frantic to find others who are compatible with innocence.

Road has secretly taken over the control of one of the five generals, and no one seems to be aware of it. The general has secretly brought in brokers to join the Clergymen, having them find ways to secretly bring down the Black Order. The clergymen are all held within the Asian Branch, and because of this, the European Branch is beginning to grow suspicions on why the Asian Branch is holding so many secrets. The European Branch is sending off various Exorcists to the Asian Branch to "spy" on them, but act as though they were being temporarily transferred.

The hopes for the Noah Clan are for the two branches to break out on civil war with one another, distracting them from their actual goals. This gives the Noah and Akuma the upper hand, allowing them to search for innocence as the Exorcists continue to fight, tearing each branch apart.

The Akuma are as if they are their own race now. There are so many of them rising, it is as though no humans are detectable through the cities, and their numbers continue to grow larger. The Exorcists only hopes are to find more Exorcists and kill as many as possible.

While hectic fights between Akuma, Noah, and Exorcists go on, an unlikely crew is starting to create their own dilemmas. Civilians are leaning witchcraft and sorcery so that they may fend for themselves when the dark age approaches. Some are good, but most are evil, taking advantage of this dark magic to become a supreme ruler.

What role will you play? What side will you join? Where will you be when darkness reigns?
...What if you possess the Heart Innocence?...