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.

Allen sets out to recover Innocence discovered in southern Italy. When a powerful Akuma attacks him, the exorcist comes face to face with something eerily familiar.

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".

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.

Allen, Lenalee, Lavi, and Krory arrive at the Bosphorus Strait but a storm delays them from going further. A cat leads them to an inn, but during the night an Akuma attack prevents them from resting. Indeed, the cat is seen with the Millennium Earl, and taking orders. It seems that lurking and plotting to kill the exorcists is the beautiful blonde Noah, Lulubell, and her Level 2 Akuma servant, Mimi. When Lulubell reveals herself, the rest of the exorcists realize their trip was going to be more difficult then ever now that they had a new Noah to deal with.

The exorcists explore the oriental world they find themselves in, but are far from being able to relax. Lulubell initiates a devious trap to separate the exorcists in an attempt to eliminate Allen and stop them from reuniting with General Cross. She seizes her chance when Krory gets himself lost, and impersonates as Lenalee to lure him to the outskirts of town. Krory is nearly defeated by her akuma, but the other exorcists arrive just in time. In the struggle, Lenalee and her imposter became confused, and both of them are captured by Akuma who then take separate paths. Allen and Krory go after one, while Lavi goes after the other, forcing the group to split up and rendering Allen and Krory lost.

Allen and Krory, having been separated from Lenalee and Lavi, arrive in a town and meet a boy named Selim, who is accused of stealing a stone statue, which is the town symbol. Everyone seem unwilling to believe him, except the mayor's daughter Karya. The villagers threaten to kill Selim, but Allen senses Akuma and destroys them in front of the villagers. Afraid, the villagers chase the exorcists back into the forest, as planned by Lulubell and Mimi. That night, Selim tells Allen and Krory how he witnessed the stone statue moving; suspecting Innocence the exorcists decide to investigate. They spot the stone statue moving into a ruined temple, and they follow it, where they become target of Mimi's Akuma.

Lavi races against time to try and make it to Bookman's location to cure Lenalee's illness, and in the canyons saves a young maid from an akuma. The maid is actually Mimi, who plots to steal Lavi's Innocence and kill them both. Luck doesn't seem to be on her side, Lavi always managed to directly or indirectly stop her from stealing his weapon. Lenalee's condition is worsening, and she tells Lavi to leave her but he refuses. The situation stirs up memories in Mimi of her own creation, and she becomes more determined to finish the mission and see Lulubell smile. She finally manages to steal Lavi's Innocence and attempts to kill the two exorcists, but Bookman's arrival turns the favour back on the exorcists' side. A defeated Mimi returns to Lulubell, who decides not to dismiss her. That is all it takes for Mimi to smile once more.

Kanda, Marie, and General Tiedoll arrive in Czechoslovakia where they meet a man named Klaus, who tells them the history of Jan Novak's famous mansion. The exorcists soon discover a trio of Level 2 Akuma who lure them into Jan's mansion, and utterly, a trap. The mansion is full of tricks and twists, along with hoards of Akuma to fight if you're not careful. With Tiedoll curiously poking around and Klaus' interference, Kanda and Marie have their hands full just protecting them.

In order to be reunited with Lenalee, Lavi, and Bookman, Allen and Krory must cross the Himalayan Mountains, in spite of a snowstorm. Behind the scenes, Lulubell sets up her plan to deceive the exorcists and trap them on the mountains forever. Impersonating as a young guide, she takes the two exorcists through a 'shortcut' in the mountains, then uses the weather as an excuse to set up tent. That night, both Krory and Allen sees the illusion of their loved and feared ones: Eliade and Arystar Senior for Krory, Mana and Cross for Allen. Eventually after an akuma attack and then an avalanche, the group finally reunites, but Lulubell states an almost sinister fact regarding their mission.

After Allen, Krory, Lenalee, Lavi, and Bookman are reunited with each other, they arrive in a town where a strange phenomenon is causing a water shortage. They soon discover a girl named Mei Ling and a history with a crystal ball that might be the cause of the water shortage and a possible Innocence. Also searching for the possible Innocence is two Level 2 Akuma.

The exorcists race to save Mei-Ling from the two Level 2 Akuma who have kidnapped her in an attempt to steal the Innocence. After some rough encounters, Mei-Ling is too frightened to do anything, and Lenalee offers her the chance to simply walk away. Upon hearing the explanation about exorcists and akuma, Mei-Ling finally accepts her destiny as an exorcist and an Innocence compatible user. At the end, disgusted by the akuma's failures, Lulubell orders it to self destruct.

Annoyed that another Innocence has reached its compatible user, the Millennium Earl orders Lulubell to investigate the new Innocence. Sensing that the Noah is frustrated, Mimi offers to do the job for her, and gets to keep a bell of Lulubell's. The scouting akuma are foreshadowed by Mei-Ling's Innocence and this allows the exorcists to defeat them all, so Mimi decides to try stealing the Innocence before attacking any of the others. Things do not go as planned and she ends up in a fight with Lenalee. Mimi decides she won't retreat this time and finally reveals her akuma form: a large dragon with the power of ferocious wind. While challenging, the exorcists' combined efforts effectively defeat her, and the Millennium Earl gives Lulubell new akuma to use instead. Realizing that Lulubell is leaving her, Mimi follows, ignoring her injured state.

Allen, Lenalee, Krory, Lavi, and Bookman accompany Mei-Ling to meet with her Finder at the Asian Headquarters. However Lulubell and her hoards of Akuma are hot on their trail. Even though she is badly hurt, Mimi decides to help Lulubell in any way she can, even at the cost of her own life.

Allen, Lenalee, Krory, Lavi, and Bookman arrive in Guangzhou, where they meet the beautiful Anita and servant, Maho-ja, who are supporters of the Black Order and who also inform the exorcists that General Cross has already left China and is heading east to Edo, Japan. However, his ship was attacked by akuma and it is unknown if he survived or not. Anita and Maho-ja decide to prepare the ship and accompany the exorcists to Edo.