Maka Albarn and Soul Eater, a Meister/Weapon pair, has defeated 99 bad souls, and they now need to defeat a witch in order to evolve Soul Eater into a Death Scythe. They seek out a witch named Blair, but there is something strange about her...

Meister Black Star and his weapon/partner Tsubaki attempt to go after Al Capone and his comrades to collect their own 99 souls but fail. Black Star and Tsubaki then learn that Al Capone plans to capture a witch named Angela and go after him once more, only to find Capone and his allies already defeated by Angela's powerful bodyguard. When Black Star decides to challenge the bodyguard, who will come out on top?

Meister Death the Kid, after failing to capture Lupin the thief due to his obsession with symmetry, speaks to his father, Shinigami-sama, and decides to go after the mummy-controlling witch residing at the pyramid of Anubis. Worried about the symmetry of a picture hanging in his room back home, Kid leaves his weapons, sisters Patty and Liz Thompson, to fend for themselves in the mummy infested pyramid. The sisters manage to defeat the mummies only to be captured by the Pharaoh! Will Kid come back in time to save them?

Maka and Soul Eater are discussing the rumors of their teacher, Sid Barett, who was stabbed in the head, becoming a zombie and preying upon the students when Maka's father comes in. As the temporary teacher replacement, he informs Maka and Soul that Shinigami wants to see them. Upon reporting to Shinigami's room, they meet up with Black Star and Tsubaki who were also called there. Shinigami tells them that because they failed to collect any souls, they would have to complete an "extra lesson". They are to find and stop Sid and the person who turned him into a zombie. They go to the cemetery, and Sid attacks them, wielding his own gravestone as a weapon. Maka and Soul attempt their Soul Resonance - "Witch Hunt" but are unable to control it properly and fail in dealing any damage. Black Star captures Sid with Tsubaki's chain, and it is revealed that Shinigami knows that the one who made Sid a zombie was Death Scythe's first partner before he worked with Maka's mother, Dr. Franken Stein.

Maka, Soul, Black Star, and Tsubaki with Sid in tow tied with Tsubaki's chain arrive at Franken Stein's laboratory and upon first appearance they think him to be just an idiot. He reveals that he can see the others' souls and he makes comments on them. After the fight starts, it is clear that Stein has the upper hand, and he shows this by nearly killing Black Star. Maka gains the power to see souls during the fight which is when she loses any confidence to continue, but Soul manages to get her back to fighting. They again attempt the technique Witch Hunt, and manage to execute it perfectly, but Stein easily dispels it, throwing them both back. Stein approaches and Soul protects Maka from him. When all seems lost, Stein reveals that the entire thing regarding Sid and himself was set up by Shinigami and therefore they were never in any danger of dying. The next day, Stein makes his appearance at Shibusen as the new teacher for Maka's class.

Late by three hours due to his routine of ensuring that every aspect at his house is symmetrical, Kid sets out with Liz and Patty for their first day at Shibusen. Upon getting there, Black Star and Soul end up picking a fight with them, and Maka, Tsubaki and Stein end up leaving class to watch their fight. The battle ends up being one-sided as Kid's extraordinary abilities proved to be more than a match for Black Star and Soul, who were unable to synchronize their wavelengths. When the duo seems to be utterly defeated, Kid ends up collapsing after realizing that Soul's last attack ended up cutting away a bit of his hair, ruining its symmetry. While Shinigami appears to take his son home, Maka tries to use her soul-seeing ability on him, but gets flustered to not being able to see his soul, unable to perceive that it is in fact big enough to envelop the entirety of Death City.

Soul and Maka arrive in Italy to dispose of another evil human. After the job is completed, Maka senses a strong energy coming from inside a church and the duo decide to investigate it. There, they meet Chrona, an evil weapon meister and Ragnarök, the mysterious sword which emanates from Chrona's body. During their fight, Maka figures that she cannot cut down Chrona as Chrona's blood has the property of turning solid, and to complicate matters, Chrona's attacks cannot be blocked as they can hurt Soul even in his scythe form. Soul urges Maka to continue fighting, but she is afraid of hurting her partner, and in the end, he receives a severe blow while trying to protect her.

Just when Maka and Soul are about to be killed by Chrona, Stein and Death Scythe appear to save them. By combining their strength, the duo have some trouble against Ragnarök's ability to transform every bit of its blood into a weapon, but in the end Chrona is defeated. The witch observing the fight reveals herself and rescues Chrona, while the others return to Shibusen in order to treat Soul's injury. Stein tells Maka that the treatment was successful, but he confesses to Death Scythe that Soul's body was infected with a demon weapon's blood, and his future is uncertain. In the end, Maka is comforted by Tsubaki and Medusa, a teacher in the school who is in fact the witch who attacked them.

After continuous failures to collect any soul at all, Sid orders Black Star to clean up the school's library as punishment. There, he meets Kid, and both learn about Excalibur, a weapon whose powers are said to be legendary. The duo decides to search for Excalibur himself, but when they find him, they cannot stand his unbearable personality. Meanwhile, Death Scythe tries to cheer Maka up, who is still worried about Soul, and explains to her the origin of the demon weapon Ragnarök. However, he still hides from her the truth about Soul's condition.

Tsubaki and Black Star are assigned the task of collecting the soul of Masamune, a demon blade who can possibly become a demon god. After arriving at the village where Masamune was last seen, Black Star is ostracized by its inhabitants, and later he explains to Tsubaki that it was because he is a survivor of the murderous Star Clan, which were destroyed by Shibusen after they started to collect human souls. The duo returns to the village after Masamune possesses the body of a young boy to confront him. Black Star manages to break the boy free from the sword's control and Tsubaki sends her spirit into the demon blade to confront the soul of Masamune, who is in fact her older brother.

While Tsubaki confronts Masamune inside the demon blade, Black Star gets himself beaten by the villagers, but he refuses to fight back or leave her side. Masamune states that Tsubaki is not fighting him seriously and that he always hated her passive behavior. He also claims that the fact of her inheriting their family's techniques and not him, was what led him to become a Demon God candidate. Just when Tsubaki was about to be absorbed her brother, Black Star's voice reaches her, and she gains the will to defeat him, absorbing her very first soul in the process. Back at Shibusen, Black Star shows to the rest of the gang Tsubaki's new form she obtained after defeating her brother, the form of a blade, but he ends up fainting as his powers are not strong enough to handle it yet.

Soul reveals to Medusa that since his battle with Ragnarok, he has continuous nightmares featuring an imp-like creature and Maka. Medusa tells him not to worry, but deduces that it could be linked to Soul's body being infected by Ragnarok's blood. Meanwhile, Stein gives Black Star a cup with a mysterious liquid as part of his training to cope with Tsubaki's new abilities, but when Maka asks him to have a special training too, he states that there is still something she is missing, and must realize what it is first. Elsewhere in the city, Medusa gets cornered by Eruka Frog and Mizune, two other witches who suspect of her intentions, and decided that she is too dangerous to live. However, Medusa reveals to them that she previously had implanted magic snakes in their bodies and easily kills Mizune. Eruka manages to escape after Maka and her friends appear to investigate.

Eruka frees Free and he quickly takes down a hoard of guards before escaping, revealing that he is immortal. Meanwhile, Maka and Soul attempt to grow stronger through Stein's training method, starting by insulting each other, which causes great tension between the two. Maka, Soul, Black Star, and Tsubaki travel to London only to run into and face Free, who further reveals himself to be capable of ice-based magic and is a werewolf. Black Star exhausts himself early on using the new Fey-Blade mode of Tsubaki, while Maka cannot initially use Soul due to their disagreeing wavelengths. She eventually fights past the pain of wielding Soul and, with Tsubaki's advice, the two reform their bond and are able to merge their soul wavelengths.

At Shibusen, tomorrow is the day of exams. Throughout the night, Maka and Tsubaki are the only ones who study diligently, although Soul seems to also be taking it seriously. Black Star attempts to steal the answers from Stein, but is caught, beat, and forced to fail. Liz and Patty attempt to study, but succumb to laziness, while Kid, confident in his knowledge as a shinigami, focuses on drawing blueprints to remove one of Liz's eyebrow hairs. During the test, it is revealed that Soul spent the whole night wiring his clothes with cheat strips, but is caught and fails from lack of knowledge and help. Kid also fails, because he spends the entire time trying to write his name perfectly, only to pass out when accidentally tearing his paper. Liz and Patty also score rather low, but Tsubaki does well and Maka ends up being top of her class.

Death the Kid, Liz, and Patty have arrived at a recently attacked coastal town and find that half the place is completely gone, as if consumed. When they discover a large ship in the fog, Kid thinks that this is the Black Dragon and observes that the vessel is named the Nidhogg. Once they eventually get on, they find no one around. Kid manages to find the room containing all of the human souls that had been gathered, but before he can do anything, the captain attacks and orders the ship to swallow Liz up. Liz finds herself alone in the bowels of the ship and decides to find her way back to Kid and Patty, in the process trying to talk through her fears with memories of her past. She reaches them eventually, but before Kid can engage the ship's captain, Ragnarok, with Chrona there as well, summons all of the human souls above deck.

Death the Kid wastes no time in starting his attack on Chrona. Liz observes that Chrona's attitude towards fear is like how the sisters were before they joined Kid. The fight gets interrupted when the captain of the Nidhogg fires the ship's cannons, Chrona cutting the ship in half in retaliation, and the ship starts to sink. Chrona and Ragnarok make their escape, and Kid tries to give chase, but they are able to get away. Back at Shibusen, Medusa reports to Maka that her blood test came back normal. She gives Maka some weird medicine that will speed up the effects of the black blood and reveals to Maka that Soul had come to her about his dreams. This makes Maka angry because he had not told her about it. The tension builds between Medusa and Stein when Medusa tries to find Maka's file so that she can figure out why the black blood is gone.

Armed with the legend of Excalibur, Ox Ford visits the cave where the sword sits and easily pulls it out of the ground. Excalibur turns out not to be what Ox expects though, as the sword hardly lets Ox speak and is more concerned about telling his own story. Ox is eager to hear Excalibur’s heroic tale, but Excalibur goes off on many tangents pertaining to coffee in the morning, his family, dancing in an opera house, incorrectly solving a mystery with Sherlock Holmes and Watson, adventures with King Arthur, and the love of his life. Excalibur also sings about himself at length before finally formally choosing Ox, however, by this point, Ox has had enough and puts Excalibur back into the ground.

Since no one knows of what Sid discovered, all the students and faculty are attending a party celebrating the founding of Shibusen. Meanwhile, Medusa is communicating telepathically with Eruka when a seemingly drunk Stein interrupts her thoughts. Stein wants to dance with her, but once they start, he becomes more serious and asks her if she knows what happened to Sid. Medusa realizes that she has been found out by his words and tries to tempt Stein with a kiss, however, they are stopped by the sudden appearance of Sid that, even injured, warns everyone to get out of there quickly. Stein is concerned about Sid long enough for Medusa to escape from the party. Free charges, but Sid is able to use his last bit of strength to use a special burial technique that causes the main characters to fall through the floor, escaping the trap.

Sid and Shinigami discuss Medusa's evil plan. Shinigami explains the origin of the kishin Asura and how it developed into such a dangerous being. The group of Mizune are attacking Death City, without holding back, as Blair walks on the roofs. As she sees all the citizens injured, she is ready to engage the witches. The group underground suddenly stops, as they find Maka's father. He turns into Stein's weapon, and everyone is ready to fight. They find Medusa, and Stein creates a battle plan to find the kishin and go through all of Medusa's allies. Medusa deploys her Vector Arrow, and Kid is the first one to escape and go on. Black Star deploys the Demon Blade mode and escapes as well. Even Maka is able to go through Medusa, but the witch is not happy and goes after her. Stein will not let it be that way though, and stops her. The stage is set for Medusa against Stein and Death Scythe.

Since Maka wants to face Chrona, Black*Star rushes past and heads further down the hall. Maka immediately starts attacking Chrona, and although her punches have no lasting effect, she is happy to hear her opponents finally acknowledge her as more than just a meal. Chrona counterattacks by using her black blood as a weapon and then by performing a resonance with Ragnarok. Maka manages to withstand the onslaught and initiates a resonance of her own with Soul, and the two enemies face off with their respective powered-up weapons. Unfortunately for Maka, Chrona is able to stop Soul with just her arms and furiously strikes back.

Riding through the halls underneath Shibusen in an attempt to catch up to Eruka and Free, Kid is stopped briefly when he reaches a field of bombs floating in the air. He’s disgusted by the lack of uniformity in the arrangement of bombs, and he only manages to get past after Patty authoritatively tells him to. Back down the long passageway, Maka uses her new-found power and fighting style to go toe-to-toe with Chrona, but the madness is literally overwhelming Soul. Inside of herself, the calm Maka uses this chance to match her soul wavelength with Chrona’s, and this brings her to a desert world where she finds a young Chrona. At around this same time, out in Death City, Blair is having no problems handling the members of the Mizune family.

With Chrona still bawling, Maka is reluctant to leave her alone until Ragnarok appears and starts bullying her. Chrona gets Ragnarok to stop by punching him, but this only causes Ragnarok to turn his bullying back on Chrona. Since Chrona is handling Ragnarok, Maka and Soul are content with going on ahead. Much further down the tunnel, Kid is close enough to the Kishin that he can now feel its soul wavelength, and it nearly overwhelms him at first. He’s okay though and explains to Liz and Patty how his father had sealed Ashura in a bag made of Ashura’s own skin. Shinigami-sama had extracted all of Ashura’s blood before doing that, so Ashura’s body is starved for blood.

Knowing that he’s running out of time, Stein wants to defeat Medusa quickly, but she’s hard to catch off guard. Medusa is simply fighting to buy time, and in order to beat her, Stein has to refocus himself. She tries to tempt him again to join her, but Stein lets himself go wild and explains the madness and fear inside of himself - what he needs is the order granted by an ego-less god. Medusa eventually stabs Stein in the gut, and from that, he counterattacks with his signature Kon-i attack. Though greatly injured, Medusa thinks she has won because she’s in position to cut off Stein’s head with her Tail Snake. She is thus surprised when she suddenly freezes in place, unable to move at all. The reason is because Stein had used one of his suture techniques on her entire body. Unfortunately, Stein can’t do anything else until he releases those strings, and Medusa knows that once that happens, her Tail Snake would behead Stein faster than he can kill her.

As Maka continues to make her way towards the shrine, the newly revived Ashura gets himself adjusted into his skin. After opening his eyes and seeing Eruka in front of him, he terrorizes her with a scream before moving on. Black*Star wants Tsubaki to enter youtou (phantom blade) mode, and when she refuses because of his injuries, he decides to take on Ashura without her. He attempts to use his Big Wave attack, but Ashura isn’t fazed at all and knocks him out with a single flick of the hand. He knocks out Kid in a similar fashion by stretching out his skin like a rubber band and hitting Kid’s head with it. Ashura follows that up by using his skin as a wrapping and covering himself with it, effectively creating himself a set of clothes. He then jumps through the ceiling of the shrine and towards the surface. Maka arrives at this moment and manages to catch him by grabbing onto his skin, but when Ashura emerges above ground in the middle of Death City, she gets thrown off.

Despite all eight Death Scythes having been called, only three other than Spirit (aka. Maka’s father) have shown up at Shibusen: Justin, Marie, and Azusa. Marie in particular doesn’t want to be there and would rather get married and retire. The more practical of the two, Azusa convinces Marie not to marry a toilet. Stein meanwhile finds Spirit polishing a candle holder in order to try to score some points with Shinigami-sama because he thinks that he’s going to get demoted and transferred away after what happened with the Kishin’s revival. The four Death Scythes plus Stein eventually meet with Shinigami-sama to talk about Ashura, and Shinigami-sama explains that they don’t need to worry about Ashura’s movements so much as how to deal with his wavelength of madness. This wavelength stirs the madness that sleeps at the bottom of every person’s soul, and it’s contagious.

Since Sid has no luck talking to Chrona, Maka and Marie bring Chrona out of her room to show her around the school. Chrona, however, doesn’t think that she’d do well here, so Maka suggests composing some poetry. Unfortunately, Chrona’s poetry turns out to be so dark though that it depresses everyone who reads it. Chrona then joins Maka in on an extracurricular lesson to a golem making village where an old golem has suddenly gone berserk. When Shinigami-sama learns out about this, he finds it alarming because golems are programmed only to protect, and he suspects that it might have something to do with the wavelength of madness. He tells Sid to contact Stein about this because he’s curious about Stein’s opinion about the matter. At around this time, Stein is off thinking about Chrona when he gets visions of Medusa telling him that he’s been infected with madness.

Stein’s research leads him to the theory that a certain heretic’s soul is inside the old golem. In the process, he finds a report about an incident in the Czech Republic where half a million people saw mysterious illusions that looked like spiders, and this causes him to conclude that the heretic scattered her body 800 years ago and left her soul in the golem. This heretic was the witch Arachne, and realizing makes Stein want to go help Maka and the others, but Shinigami-sama urges patience. Arachne is the mother of magic weapons, but creating one required the sacrifice of a witch’s soul. 800 years ago, she had been pursued by Shinigami-sama and had escaped into the old golem’s chamber. Back in the present, Maka and Crona are having a hard time dealing with Giriko and the golem, and Maka finds herself unable to move her body after getting sprayed with a special silk. Spiders then appear all around them and combine to form Arachne’s body.

While Maka is still recovering, Sid gets word from Azusa about a research facility belonging to Arachne’s Arachnophobia organization. Sid and Nygus go to investigate the magic tool that’s being built, but Black*Star overhears them discussing the situation before they leave, and he secretly decides to go as well to get revenge for what happened to Maka. Unbeknownst to Black*Star, Angela and Mifune are at the research facility along with Mosquito. Sid arrives there first though and sneaks in with the help of Azusa’s special ability to map out an area. The alarms go off while he’s inside, but it’s not because he’s been discovered; it’s because Black*Star has arrived and is creating a commotion by beating up guards. Mosquito, Mifune, and Angela all head out to see what’s going on, and the latter two immediately recognize Black*Star. With Mosquito holding Angela close, Mifune has no choice but to fight the opponents he still considers to be children.

When a stray dog finds a snake amidst some garbage, the snake enters the dog. When a little girl named Rachel then finds the dog, the snake enters Rachel. Rachel’s mother notices her daughter acting strange all evening, and that night, she wakes up to find Rachel at her bedside staring at her with an evil eye. This causes Rachel’s mother to scream and wake up Rachel’s father, but Rachel is now crying on their bed, talking about some scary snake in a nightmare. The father lets Rachel sleep with them, and the next morning, she appears back to normal. When a spider suddenly appears in the kitchen though, Rachel crushes it with her hand and comments on how Arachne already noticed.

Death the Kid, Liz, and Patti have arrived in the Sahara Desert to go after a special train that has run without stopping for 100 years. It does so through a demon tool that Arachnophobia is now after, and their job is to prevent this and recover it themselves. When they arrive at a train station in the middle of the desert, there is already someone there, but this person doesn’t say anything to Kid or the girls. The train soon arrives on time, however the way it arrives is by bursting out the sand. An agent of Arachnophobia named Fisher King immediately grabs onto it and gets on, and Kid is further surprised when the other person at the station - Mizune - suddenly cancels her Soul Protect and flies after the train.

Everyone has been nice to Crona since she came to Shibusen, and this is especially apparent during a party one night. Kid is supportive of Crona proceeding at her own pace, and Black*Star promises to beat up anyone who bullies her. Since Crona isn’t sure why everyone is being so kind, Maka explains that it’s natural since they’re all friends. These warm feelings stay with Crona until she leaves the party to go home, and that’s when Medusa appears. Despite Medusa’s small body and seemingly gentle nature, Crona is deathly afraid of the witch. Medusa claims that she came to see Crona and was very worried, but what she wants Crona to do now is to spy for her in Shibusen and to find a secret vault. Crona doesn’t want to betray her new friends and new home, but Medusa uses her status as Crona’s mother to coerce Crona to do it.

A Shibusen student named Hiro who is often taken advantage of by other students has discovered Excalibur’s book and envisions himself as a hero, so he goes and retrieves the legendary sword. When Black*Star arrives at school the next day, he finds Hiro beating up on other students, and with Hiro is Excalibur. Excalibur is still his long-winded and annoying self, but Hiro can actually tolerate him and his list of 1000 things. Black*Star, however, cannot, and soon feels the urge to kill Excalibur. Both Kid and another student named Kilik want to participate as well, but none of their attacks hit, and Hiro and Excalibur defeat all three with a single move. As a result of all this, Hiro finally feels respected, and he has no trouble following Excalibur’s list of 1000 things that he has to do, such as participating in a daily 5 hour recitation and always praising Excalibur.

Though Stein is having more flashes of madness, he tells Shinigami-sama not to worry about his health. Shinigami-sama has summoned him today to talk about how Arachnophobia has discovered the location of one of Eibon’s tools called BREW. Shinigami-sama foresees a big battle and urges Stein to get the students trained up to handle it. Stein thus takes the class out to practice, but before the lesson begins, Black*Star does some private training where he attempts to understand the other existence inside of Tsubaki. This leads him to an encounter with a giant beast who asks him about seeking power, and Black*Star answers that it’s so that he can surpass God. The beast, however, sees Black*Star more as an ogre. After waking back up from this vision, Black*Star joins Maka and Kid to practice their team soul resonance. Explaining the situation to them, a very serious Stein warns them that if they don’t pass, then they’ll be removed from his class.

BREW exists on a lost island north of Alaska where there used to be a witch’s tool development facility before it got destroyed from an accident. That accident resulted in a special magic magnetic field in the center of the island - BREW is inside of there - and staying in that magnetic field for longer than 20 minutes will result in a person’s body getting destroyed. A small army of Shibusen students and staff are already headed towards the island, and the plan is to have Sid’s force take care of the Arachnophobia forces while Marie, Stein, and the students head for the magnetic field. Once there, Marie and Stein will head into the field while the students stand by outside until the two return. Things start out according to plan, however Sid’s force is soon ambushed, and Sid finds himself facing off against Mifune.

Ox, Kilik, and Kim continue fighting the Arachnophobia forces, but since they’re approaching the 20-minute mark that Stein had set earlier, Kim sets out to give the signal for retreat. Ox and Kilik work together to cover her, and Kim successfully gets away from the battle. Mifune meanwhile has walked into a trap set by Nygus and Sid, and Sid tries to hold Mifune in place while a giant pillar comes swinging down towards him. Mifune forces Sid to let go by stabbing him in the shoulder, but it’s too late and Mifune gets smacked by the pillar. Although injured, Sid then charges Mifune and stabs him in the arm. Mifune counters by digging his hand into the wound he inflicted on Sid moments ago. Neither are able to bring the other down, and since Mifune doesn’t care to negotiate, the two get ready to start another round of fighting. They never do so however because Kim and Jackie draw the retreat signal in the sky, and so Sid leaves the fight.

While everything else is going on, Justin and Giriko are having a private battle in the snow. After getting a little beat up, Giriko decides to run and distracts Justin with snow copies of himself. Meanwhile, the Mizune sisters report their success back to Eruka outside the magnetic field. Inside the field, the demon inside Soul is urging him to start playing the piano, and when Soul finally does, everyone can immediately feel the effects. The resonance link allows Maka, Black*Star, and Kid unprecedented coordination, and Mosquito barely has time to defend himself. Soul then directs each of the three to use their strongest attacks in succession, and Black*Star and Kid cause Mosquito to lose his arms. When it’s finally Maka’s turn, she transforms Soul into a form that surpasses the Majou Gari (lit. witch hunter): the Majin Gari (lit. demon hunter). This easily slices through Mosquito, but unfortunately, Mosquito detaches his head and escapes before the rest of his body explodes.

Arachne is convinced that "Brew" is defunct, when it is actually functional and in Medusa's hands. Meanwhile at Shibusen, everyone assigned on the "Brew" mission is depressed about their defeat against Arachnophobia, except Kid, who ponders about Eibon and Shinigami's association with him. He even confronts Stein and interrogates him about what "Brew" is and why Shinigami sought to possess it. Maka questions her ability of using 'Demon Hunter' while fighting Mosquito and talks to Shinigami about it. Determined to use 'Demon Hunter' again, Maka and Soul make an attempt, but they fail to do so. At the end of the day, a man named Joe Buttataki arrives at Death City at Shinigami's request.

Once he arrives at Shibusen, Joe Buttataki begins his project by using the demon tools that are in Shinigami's possession. Meanwhile, Black Star's confidence begins to waver due to his recent defeats. When Tsubaki tells that Nygus asked her to stop using the dark blade mode, Black Star decides to challenge Kid in a duel, and during which loses control. Kid finally wins the battle and shortly after Black Star starts training again. Arachne finds the hideout of Asura.

Crona is visited by Eruka again, telling Crona to return to Medusa. Meanwhile, Arachne visits Asura alone in the mountains to ask for an alliance against Shibusen. Death Scythe brings Soul and Maka to Crona's room, showing them that Crona is gone, which causes Maka to look everywhere for Crona. Crona is outside of Shibusen walking in the desert sand and falls into a hole and sits there. Back at Arachnophobia, Asura has allied with Arachne. Maka and Soul find Crona in the hole and Crona cries, confessing about putting Medusa's snake in Marie's tea. Shinigami discusses with Death Scythe and Maka about Crona's betrayal when Sid suddenly announces that Medusa has come to Shibusen to surrender.

To win Shibusen's trust, Medusa reveals the location of the real "Brew", and proposes to give information about Asura's whereabouts in exchange for her freedom and protection of her peers. When Arachne moves on with her plan to spread the kishin's madness throughout the world, Shinigami decides to accept the deal. Marie later discovers that Stein is nowhere to be found.

Stein struggles with the decision whether or not of return to home. Meanwhile, Joe Buttataki discovers a secret page in the book of Eibon, which shows it takes one last demonic tool to operate "Brew". Crona and Marie decide to search for Medusa and bring back Stein. Maka and the others, even with doubt about Shibusen, remain firm in fighting and defeating the kishin. Finally, the path that Stein is walking leads him to Medusa.

Maka is confused due to the decisions recently taken by Shibusen, which is preparing for a huge battle against Arachnophobia, to defeat it along with the kishin and destroying the six madness amplifiers. Marie and Crona are the only ones who can deal with Medusa without breaking the deal with Shinigami. Maka, along with Soul, Black Star, and Tsubaki, go to Baba Yaga's castle when Arachne gives the order of attack. Justin starts a fight against Giricco. Maka finally decides to abandon the battlefield to go to help Crona, leaving the fighting to Black Star. Meanwhile, Kid is on the way to retrieve the latest demonic tool.

The battle against Shibusen and Arachnophobia continues. Kid, Liz and Patti arrive at their destination, a town called Sekikan, whose inhabitants had disappeared mysteriously twenty years before. For the sake of his partners, Kid decides to enter the village alone. Once in, he easily finds the demonic tool, but is attacked by a strange clown. Maka realizes she must feel the soul of one of the people that she is looking for to find them. Kid is chased by the clown, who is soon joined by another one just like him. Due to the symmetrical attacks of the clowns, Kid is unable to respond until Patty and Liz arrive to help and successfully defeat them. Shortly after the battle, a mysterious person communicates with Kid, questioning Shibusen's right to use the demonic tools. Justin, Black Star, Kilik, Ox and Kim are still battling.

Maka and Soul try to seek out Crona and Marie via Maka's Soul Perception ability to find Medusa. Meanwhile, Crona and Marie manage to find Medusa's hide-out and battle with her and a maddened Stein. While Crona struggles in the battle with Medusa, and is about to be killed, Maka and Soul jump in and block the attack. Black Star continues to advance to Baba Yaga's Castle.

Maka, Soul, Marie, and Crona continue their battle with Medusa and Stein, but are being overwhelmed. Marie asks Maka and Crona to concentrate on Stein, which gives her the chance to use the Wavelength of Redemption. Medusa uses the lull in combat to target Maka with an attack. Crona pushes Maka out of way and takes the full force of Medusa's attack. Crona is greatly injured by Medusa's vector blade. Maka is consumed by the madness and attacks Medusa with full force, and disarms her; before Maka can land a fatal blow, Stein protects Medusa, and this finally provides the opening Marie needs. Using the redemption wavelength, Marie saves Stein. Maka uses her demon hunter wavelength to defeat Medusa and save Rachel. Black Star finally reaches Baba Yaga's castle to battle Mifune.

As Mifune fights with Black Star, he counts how his father was strong, but chose the wrong path and he was forced to kill him, and he asks his opponent if he's going to choose the path of the warrior or the path of a demon. Meanwhile it is revealed that the key to operate Brew is the soul of Eibon itself, who happens to be one of eight warriors of Shinigami, and who his willing to cooperate to deal with Asura. Arachne decides to leave her organization behind by putting into operation several weapons that the Baba Yaga's castle had prepared. Returning to the battle, Black Star refuses even to listen to Mifune, who, seeing no possibility of change for his opponent decides to finish it in one fell swoop, killing Black Star. Eibon finally put Brew function to work: make real the most desperate desire of one's heart.

Black Star revives, declaring that he will take the path of neither the warrior nor the demon, but will instead take his own path. He defeats Mifune with one swipe; however, he does not kill him, but instead invites him to be a teacher at Shibusen. They then go off to find Angela. Meanwhile, Eibon uses a key created from his own soul to activate Brew, which has been revealed to grant the desires of whoever uses it. Shinigami uses the Demon Tool to transform Death City into a giant robot, and swiftly enters the battle. After attempting to squish Baba Yaga's Castle to little success, it manages to reach inside of it, grab Asura, pull him out into the open and "eat" him, apparently trapping him inside the city.

Upon being devoured by the Death City mecha, Asura lands in the Death Room, where he is confronted by Shinigami and Death Scythe. Meanwhile Black Star, Tsubaki, and an injured Mifune find Angela in Baba Yaga's Castle. Shinigami and Asura begin to battle while Kid, Azusa, and Excalibur observe. As they fight, Asura begins to explain why he does what he does. He believes that all fear in the world is the result of people's imagination. Asura claims to no longer imagine, and plans to end all fear by spreading madness and preventing people from imagining again. Shinigami disagrees with him, and declares that he is this world's guardian. Shinigami appears to have the upper hand until Asura fires a large blast from Vajra at Kid and Azusa. Shinigami blocks the blast with his body and is gravely injured.

Asura, being injured from the battle with Shinigami, begins to put up a barrier around himself preparing for a deep sleep. Before the barrier closes, Maka, Black Star, Kid, and their weapons are the only ones able to get inside. Having devoured Arachne's soul, Asura grows tremendously in size and strength. When the fight against Asura begins, they do not appear to be injuring him, but Kid thinks they are as the barrier is weakening. They start a chain resonance with Soul playing the piano, but when Maka is about to perform Demon Hunter, Soul pushes himself too far and is devoured by the black blood. With Soul, the only one who can help them do a chain resonance, down for the count, Maka goes to bring Soul back, with Black Star and Kid protecting her.

While everyone outside the barrier can only sit and wait anxiously, Kid and Black Star continue to battle Asura with almost no results. Determined to avenge his father and protect the world, Kid begins soul resonance with Patti and Liz, but he is stabbed by Asura and falls to the ground. Seemingly dead, Kid's eyes suddenly fill with a blue light and his soul becomes extremely powerful as he transforms Liz and Patty into a huge double cannon. Using his speed to his advantage, Black Star attacks Asura and Kid follows with a massive cannon explosion. With so much power however, Asura still stands, though he has changed form again. Meanwhile Maka is locked in a room with the demon disguised as Soul. However, Maka realizes he is a fake. Risking being devoured by the black blood, she decides to open a locked box to free the real Soul.

As the two realize that the kishin was still undefeatable, Asura confronts Maka and Soul. Maka's last hope of defeating Asura was her anti-demon wavelength and demon hunter. But still Asura can deflect all of her attacks. As Asura shoots at her, Soul blocked the shot himself to defend his partner and knocking him unconscious. Maka attacked him and was easily defeated, as Asura was going to finish the job, he noticed that Maka has developed the ability to transform into a weapon. Still Asura can deflect her attacks, but Maka was relieved since she's not afraid of anything now, giving her more courage that causes the Kishin to wonder what courage means. Asura felt fear as Maka was approaching him and giving her last blow.