Allen Walker and his golem, Timcanpy have recently arrived in London, planning to visit the Black Order Headquarters. Meanwhile, Officers Moore and Charles are investigating a supposedly haunted church. While searching this abandoned building, Moore and Charles are separated due to Allen's "kidnapping" of Moore. After he is handcuffed to a chair, Allen tries to explain his situation to Moore when Charles is suddenly killed. Since Moore was unconscious due to the attack, Allen is suspected of Charles's death. Allen attempts to tell the chief that an akuma killed Charles and that he would like to help. However, due to the disbelief of the chief, Allen is placed under house arrest while the rest of the police unit investigate the church themselves. During his stay at Moore's home, Allen explains to Moore about what is akuma and later on, he meets Moore's brother-in-law, Mark who is the akuma that killed Charles and countless others who visited the church. Upon investigating, Allen finds out that Moore's sister, Crea is the soul entrapped in the akuma. The akuma later kills the police units excluding Moore and later, Allen destroys it by using his Anti-akuma weapon.

Allen finally arrives at the Black Order Headquarters. Due to a misunderstanding, everyone thinks he is an Akuma. Yu Kanda confronts Allen and damages his anti-Akuma weapon. Eventually, it is resolved when Komui finds a letter of introduction from Allen's master, Cross Marian. Afterwards, Allen is allowed into Headquarters and is given a tour by Komui's sister, Lenalee Lee. After getting his arm repaired by Komui, Allen is examined by Hevlaska, an exorcist who is able to measure his synchronization ratio. In addition, she predicts that Allen will create a powerful "Destroyer of Time" in a dark future. From Komui, Allen learns more about the war between the Earl and the Innocence. Reever Wenham, the unfortunate assistant to Komui, is introduced in this episode as well. We also get a glimpse of Allen's "dark" yet comical past with Cross Marian.

After Komui wakes up from his nap, he assigns Allen and Kanda on a mission to investigate strange occurrences in the ruins of a town called Mateel, located in Southern Italy. An Innocence is discovered there, but it is in danger of being taken by the Akuma. There is a legend that a ghost roams Mateel, killing anyone who wanders near it. The ghost is somehow connected to the Innocence. Along the way, Allen talks to Toma, a Finder, who told him about how strange occurrences in history are usually related to the Innocence. Meanwhile, the Finders in Mateel capture two Akuma in barriers, but they are attacked by a third one. Shortly after the two exorcists and Finder arrive, they witness the Akuma attacking the last remaining Finders. While Allen runs to fight the Akuma and tries to save the Finders, Kanda rescues Guzol and Lala, whom the Finders protected in a barrier. During Allen's fight against the last Akuma, the Akuma evolves to Level 2. Kanda refuses to help Allen and leaves with the Mateel residents to a safe place. The episode ends with a stunned Allen being attacked by another Allen.

Allen continues his battle with an Akuma that has leveled up and gained the power to take on a person's appearance and powers. Meanwhile, Kanda hears from the "Ghost" of Mater the history of the town and the Dolls they made to cheer themselves up.

The adventure in Mater draws to a close as Allen and Kanda discover the truth of who the Doll actually is and then battle the level 2 Akuma for possession of the Innocence.

On his way back to the Black Order headquarters from Mater, Allen meets a boy named Jean. Jean and his friends have organized a patrol to search for Akuma within the town. Allen warns the boy that this is dangerous, but Jean won't listen.

Allen's past is revealed as he confronts the Earl of the millennium, who wants to kill Jean for causing problems with his patrol and calling the Earl "a bad guy".

Komui's latest invention, Komurin II, is designed to make exorcists stronger. However, Komurin II goes out of control and starts hunting the exorcists within the Black Order. Its all the scientists can do as they try to stop the robot from capturing Allen, and despite his experience with Komurin I, Kanda refuses to help. Meanwhile outside of the Black Order, the Millennium Earl holds a dinner with several strange humans with golden eyes and crucifixes on their foreheads, one of which is a young girl with spiky dark hair.

Allen and Lenalee are sent to investigate a town where the day of October 9th keeps repeating itself. Once there, they meet a woman named Miranda Lotto and thus learn of her significance to the strange phemonenon of the town. The Millennium Earl announces to his family, the Noah Clan, that it is time for them to head out and continue their mission, thus leading one of the Noahs, the young spiky haired girl Road Kamelot, to investigate the Rewinding Town.

Allen and Lenalee resolve to help Miranda in order to prevent time from repeating itself. Unbeknownst to them, Road has been watching their every move and has special plans for them.

The terrible realization that Road Kamelot is a human horrifies Allen, who cannot understand why a human and akuma work together. The talking umbrella Lero chastises Road for going against the Earl's plans, but Road points out this little incident was only to 'spice things up'. To prove herself as different from regular humans, Road stabs herself with Allen's Innocence, only to recover right in front of him quickly. She stabs Allen in the cursed eye, and makes to kill Miranda, but Allen rescues her. Through this Miranda has a realization about herself, which causes a reaction from the Innocence.

Thanks to Miranda's Innocence, Allen and Lenalee temporally recover and fight for survival against Road and her Akuma. Just when things seem to be going well, Road decides to torment Allen by ordering an Akuma to self-destruct, explaining that an Akuma who dies this way will never be saved and their soul will be forever lost. Desperately, Allen tries to exorcise the Akuma before it happens, but Lenalee stops him, and the Akuma explodes. The soul is seen begging for Allen's help, and he takes out his anger on Lenalee, who slaps him before telling him as a friend she had to stop him. Road laughs at the scene before leaving, and Allen tries to stop her, but is unable to bring himself to kill the Noah. Road leaves the dimension promising Allen that they will meet again. The Exorcists, along with Miranda, return to Miranda's home.

The battle with Road is finally over and Allen is unsure on his reasons for becoming an exorcist, but after meeting a new exorcist partner, Lavi, his sense of reason returns to him by understanding the significance of wearing the exorcist uniform.

Allen, Lavi and Kanda are sent to investigate a mysterious rapid snowstorm, which could be due to Innocence. Here they meet a young girl and her father, who is obsessed with finding something called The Leaf of Revival to bring back his dead son. Meanwhile, also searching for a possible Innocence in the same area are three Level 2 Akuma under the command of a Noah named Skin Bolic.

Allen, Lavi and Kanda continue their search for the Leaf of Revival, which they assume to be the Innocence. After realizing it is Innocence after all, the three Level 2 Akuma attack to retrieve it from them.

While searching for an Innocence in Rome, Kanda encounters a mysterious swordsman named Victorio, whose power is unbelievably strong. When Kanda hasn't returned after a while, Komui asks Allen and Lenalee to go to Rome to investigate why Kanda is taking so long, thus they learn the history of Victorio and the Princess, whom he vowed to always fight for.

Allen, Lenalee and Kanda find themselves in a predicament when they battle Victorio. How can they stop someone who apparently cannot die from shear wounds?

Seeing Lenalee and Russell going out together, Komui assumes that they are dating and in rage, chases after them with his newly built, Komurin v2. Concerned, Allen, Lavi and the Science Division work together in an attempt to stop his reckless behavior. Meanwhile, an Akuma with amazing transformation skills has targeted Lenalee, but keeps being on the receiving end of Komui's explosive inventions.

While on a mission to search for General Cross, Allen is beseeched by several villagers complaining about a "vampire problem." Soon after the ruckus, Lavi and Bookman join Allen on his new mission.

Allen and Lavi decide to investigate Arystar Krory, the vampire who is supposedly terrorizing the village. They head up to Krory's castle and meet his beautiful lover, Eliade.

When Allen and Lavi discover the truth about Krory's attack on the villagers, he appears before them with an intention to fight, thus leading to a rather fierce battle.

While Lavi and Krory continue their battle outside the castle, Allen finds out the truth about Eliade.

Devastated by what he just learned about Eliade, Krory decides to fight her, despite his feelings toward her. Finally, Eliade is defeated and Krory decides to become an exorcist.

After finishing the mission that General Cross left for them, Allen and Lavi accompany Krory back to Headquarters so he can be inducted as an official exorcist. Krory is inexperienced to the outside world, and is very easily deceived by others. He soon gets hustled in a game of cards by a rag tag group of three men, and Allen proves his cheating skills when he wins everything back. One of the men, Tyki, gives Allen a pack of cards before they leave; but this Tyki is soon revealed to be an ally of the Millennium Earl and a Noah.

Having been sent by Komui to deliver a package to General Kevin Yeegar, Allen arrives at Holland, but the general does not show up. Finding out that General Yeegar went to Belgium to investigate a newly-discovered Innocence, Allen heads for Belgium as well. There he meets Yeegar for the first time and discovers what a nice and kind person he truly is.

The Millennium Earl makes an announcement that the next chapter in this wonderful story is about to begin as General Yeegar is confronted by Road Kamelot and Tyki Mikk, two of the Noahs, along with a hoard of Akuma. Allen meets Lenalee and the two discuss the kindness of Yeegar, but soon receive a phone call from headquarters telling them to support Yeegar. Yeegar proves himself more then capable of dealing with the Akuma, but falls victim to his own memories of his tragic class. Road sings an eerie song about the Earl's search for the Heart of all Innocence, and when Exorcists finally arrive to where Yeegar is, her song is the only thing he can say. Komui is forced to explain what the 'Heart of all Innocence' is.

After General Yeegar's tragic death, Allen, Lenalee, Lavi and Krory are separated into two groups and sent to look for General Cross and guard him from the enemy. During this time, Allen tells Lenalee his bitter memories of Cross and the tragedy of a good friend.

Krory, Lavi and Bookman come upon several villages where people keep disappearing. They soon learn of a possible Innocence and a mysterious Level 2 Akuma. The Akuma works on the farm and plays with the children, and Krory lowers his guard as he believes in the possibility of 'good akuma' like Eliade. When it seems as there is another Akuma, Krory goes after it viciously but the Akuma escapes. When the truth is revealed, Krory is forced to accept the fate of being an Exorcist.

The Millennium Earl is seen bouncing about cheerfully, answering several phone calls and confirming business deals. Allen and Lenalee arrive at Liverpool to meet Mother, who took care of Allen during his training years with General Cross, to ask her about his master's whereabouts. Both exorcists soon discover akuma in the area and a possible conspiracy at a local hospital.

While Allen comforts Lisa as she mourns her sweetheart's death, Lenalee investigates the cause of why there is a large quantity of akuma in the area, thus revealing the work of a Broker, who sells souls to the Millennium Earl. There are two suspects, the chief doctor, and a young money-hungry one. Working undercover as a nurse, Lenalee is determined to find out who.

While heading off to Headquarters to become an exorcist, Miranda gets separated from her Finder escort. Here she meets a nice travelling family who takes her in, however, when Akuma discover her Innocence, they mount her but Officer Moores saves her just in enough time for Lenalee to come and rescue them both.

While waiting for a ship to rendezvous with Lenalee, Allen encounters a group of wannabe pirates who claim that a pirate ship is sinking ships along the coast.

While on his way to meet up with fellow exorcist, Daisya Barry, Kanda hears a rumor about "The Forest of No Return" and discovers he must pass through it. There, he meets a Finder named Gozu and soon comes upon a village where, according to a legend, a witch is supposed to live.

Kanda and Gozu discover the truth about the legend of the witch and Sophia's tragic past, which leads to a fierce battle.

As she is on her way to reunite with Allen, Lenalee agrees to accompany Gozu to the next town. However, in the midst of the forest, they meet a group of stranded villagers, running away from their home because of wolf attacks. The wolf attacks are revealed to be the work of Akuma and Lenalee receives help from Suman Dark, an exorcist and long time friend, who is searching for General Zokalo.

Continuing their search for General Cross, Allen and Lenalee get attacked by Akuma and bump into a group of Finders. Meanwhile, at another breakfast gathering, The Millennium Earl announces to the Noah Clan that he's come up with a plan to get rid of the exorcists. He gives Tyki, Jasdero and David (Twins), and Skin a card with names on it of whom he'd like them to kill and get rid of.

As Kanda and Daisya head out to Barcelona to meet up with General Tiedoll, Daisya reminisces about his past on how he became an exorcist and how he met General Tiedoll.

With there destination not too far away, Kanda and Daisya meet up with another fellow exorcist, Noise Marie, and together they head for Barcelona. Meanwhile, a massive attack from a legion of Akuma brings crisis in Barcelona where it is thought to be the location of General Tiedoll. In fact, he is travelling with a family and still sketching landscapes. The large groups of Finders struggle to protect the city as they wait for the exorcists to arrive, but are ultimately overwhelmed. Luckily, Kanda and the others arrive just in time, but to their misfortune Tyki is in the same area. While the Exorcists are split up, Daisya meets Tyki and realizes Tyki is not human.

Daisya attempts to fight Tyki, but is no match for the powerful Noah, thus leading to a tragic conclusion. Meanwhile, Allen and Lenalee rush over to Barcelona when they heard that it had been attacked. When they arrive there, they find the bodies of their comrades. Meanwhile, Kanda and Marie finally meet up with General Tiedoll. Tyki gets himself lost, and meets up with Suman Dark and his teammates. The tragedy of the war is escalating, even the Noahs appear sober in comparison to their previous antics. Back in the Black Order, Komui is forced to show a more ruthless side as he forbids the Finders from telling the decreased's families of the deaths. Tiedoll and his exorcists briefly meet Allen and Lenalee, and tells them that Timcampy could be their guide for Cross.

Following Timcampy on the continued search for General Cross, Allen and Lenalee reunite with Lavi and Krory in a town celebrating the Rose Festival. Lavi tells them the total number of casualties, and how one of the Exorcists were killed by a Noah. Meanwhile, Road is seen abusing Lero, while the Millennium Earl talks about his concern with General Cross. During the night, Allen remembers the people he could and couldn't save. He cannot stand the fact that he can't protect his companions, but with the help of Lavi, realizes the true reason for why they fight. The next day as they make to leave, a beautiful blonde woman is seen watching them.