The main character, Allen, is infected with the spirit/soul of the 14th Noah by his adoptive father Mana. The 14th Noah betrayed the other Noahs, who are the bad guys, and tried to kill the Millenium Earl (the 1st Noah). But he didn't do it to save the world. He did it so he could become the Millenium Earl, so he could become the leader. Mana was the 14th's brother, and when the 14th died (killed by the Earl), Mana pretty much lost his mind. Mana was a rodeo clown, and the main character was abandoned as a child because his right hand was deformed (a parasitic innocence). Mana took him in, and "pretended" to be a loving father (though we really don't know the circumstances just yet, because this was a recent development). The 14th's personality slowly starts taking over Allen's mind and body. Allen pretty much woke him up when he stabbed himself with his evil-destroy sword (his sword can only hurt akuma and Noahs). The Millenium Earl also wants the 14th to come out of Allen, because he still considers him his family, and all that good stuff.

Also, one of the main characters was actually created in a lab. The church was doing experiments to revive deceased excorcists, because excorcists are really special people who can synch up with a specific innocence (the weapons excorcists use to kill akuma and Noah). They figured if they could revive them, then they would maintain their ability to synch with their innocence. They have really special bodies, which are pretty much immortal for a certain period of time. They can regenerate really quickly, even removed limbs. Almost all of the experiments had to be destroyed, because they would regain their memories of their life, which would infect their minds, and they'd pretty much go crazy. Kanda, the main character, has memories of his lover before he died, and we actually find out later that, in his mind, he is constantly surrounded by a garden of flowers. Like, the walls, the floors, etc... in his mind, they are all covered in flowers.

A more recent development was that, when Kanda was a kid, and he was being taught to synch with his innocence and stuff, and they were doing experiments, he had a friend who was the same as him. Later on, his friend finds out what they are, and he kills all of the scientists and stuff working on the project. He even regains all of his memories, though Kanda doesn't. It turns out the spirit implanted into the boy was Kanda's dead lover from before he died, who was also an excorcist.