The group waits outside Dr. Stein's labratory as they note the odd structure of the building. Wondering what kind of person Stein is, the doors fly open as Stein falls over on an excutive chair, cursing that he doesn't feel right as he twists the screw in his head. He attempts to stick the landing with his chair, but continues to mess up again and again. Soul asks if Stein was the man who turned Sid into a zombie, to which Stein deduces that they must have come from Shibusen and they are there to attack him. Stein is able to see their souls in a physical form as he analyzes what kind of people each of the kids are. After butting heads with Black Star briefly, he goads them into fighting as the battle commences.
At the cabaret, Death Scythe is seen drinking with Blair, who has a new job at the gentlemen's club. Blair comments how happy Death Scythe seems to be when in truth he is upset since the divorce with Maka's mother was finalized. He also laments on how his daughter is fighting Stein and points out he used to be Stein's partner before switching. Stein confirms this to Maka when fighting as he refers to Death Scythe as Spirit, his name before he made the transformation. Death Scythe claims that no matter what, Stein is a pure genius and knows how to fight. Back at the labratory, Maka tries to rush Stein but Stein shows he is able to use his own soul as a weapon, disarming Maka and figures out how to experiment on her. Black Star reemerges as he shows he knows how to use Soul Force too. However, this barely damages Stein as he able to attack Black Star at point blank, apparently killing the young boy. Death the Kid and Shinigami-sama watch from the Death Room as Kid claims he is going to help the group. Shinigami-sama tells him that he shouldn't interfere with the affairs of the students of Shibusen. Kid promptly requests to be enrolled as he takes the Thompson sisters with him to fight. But his neurotic behavior kicks in before he can get there since he debates on if he folded the toilet paper correctly.
Tsubaki tends to Black Star as Maka and Soul try to fight Stein again. In the midst of the fighting, Maka is able to see souls the same way Stein does, collapsing at the sheer sight of it. Soul chides her as she can not determine her future by simply viewing the soul of another person, trying to convince her to make him a Death Scythe as promised. Maka is able to get some courage as she and Soul perform a soul ressonance, attempting to take Stein down with the Witch Hunter. Stein marvels that they are able to use is so well, but shows his strength by being able to stop it in its tracks and destroy it. Maka falls to the ground as Soul flies off. Stein commends her for still being conscious after the attack and debates on how to dissect her. Soul transforms back into a human to protect Maka from Stein, telling the scientist to back off. Stein comments that he'll start with Soul and announces the group passed their remedial lessons. In truth, Shinigami-sama asked him to help out and Sid was in on it too. Soul comments about Black Star's death, but the boy turns out to be alive, just was unconscious. Soul and Maka wonder what the point was as Stein admits it was fun to scare them and invites them to stay overnight. They refuse and return to their homes for the next day of school. It turns out though that Stein is Sid's replacement as teacher for the class as the group laments over the new change.
Death the Kid goes over every inch of his mansion, noting the symmetry he has made and how perfect it all is. He bids the Thompson sisters to come with him to his first day of lessons at Shibusen, to which Liz responds that they are roughly three hours late. At the school, rumors are floating about on who the new student is as Stein starts class, noting how Soul and Black Star are both absent. Maka just claims the two are lazy as Tsubaki worries on if Black Star will ditch her in favor of being Soul's new partner. Outside, Kid approaches Shibusen as he admires the perfect balance of his father's school as he notices Soul sitting outside the school. He wonders if Soul is there to give him a tour of the school as Soul tells him that classes started at 7 am, which greatly troubles Kid. He notes that 7 is imperfect and begs Soul to change the number to 8. Black Star, in his normal manner, is perched on a spike as he announces loudly his plans to defeat the son of Shinigami-sama. However, he breaks the spike, which annoys Kid moreso since Black Star has thrown off the symmetry of the school. Kid gets the Thompsons to turn into guns as he fights the two.
The students in class hear the commotion as someone notes Soul and Black Star fighting the new kid. Maka, trying to get Stein to stop a dissection of an endangered bird, reminds Stein that professors must oversee battles between students. Stein reluctantly stops as he brings Maka and Tsubaki to stop their partners. Outside, the two students try to get in attacks, but Kid shows he is brilliant in both short range and long range combat, demonstrating his ability to use the Thompson's soul bullets. When the three get outside, Maka notes how difficult it is to maintain two weapons at the same time. Stein tells her to look at their souls as Maka see how perfectly balanced Liz and Patty are with Kid. Stein points out that Kid helped the girls out of the streets of NY and the girls keep his OCD on balance in check, fully beneficial for one another.
Black Star tells Soul to turn into a Scythe but the two are not compatible with one another as Black Star damages Soul with his soul energy and Soul accidentally stabs Black Star in the head (mostly due to the latter not being able to catch the scythe). Soul announces they shouldn't work together like this anymore, which saddens Black Star since he thinks he can't be friends with Soul anymore. Soul cries as he tells Black Star off, statin loudly they will still be friends. Kid interupts as he activates Soul Ressonance which causes the Thompsons to transform into the Death Cannons, unleashing a massive blast at the two. However, afterwards Kid collapses as Maka remembers that Soul got in a very small attack, cutting off a few strands of Kid's hair, which threw off his balance. The Thompsons help Kid up as Shinigami-sama came to see how his son was doing, but vows to take him home. Maka wonders what Shinigami-sama's soul looks like and notices there is not one there. She guesses that he might not have a soul as a massive soul appears over Death City.
As night falls over a city in Italy, a witch is seen on her broomstick as she telepathically goads a young woman in the middle of the city to kill as much as she can. In a church nearby, this girl is seen with a black sword as she talks to herself about how the doors only open inward as a group of humans attempt to jump him. She uses her ressonance wave which is called Scream Ressonance as the humans are attacked by the figure. A few blocks down the road from the church, Maka and Soul are seen collecting a Kishin soul as part of a lesson and are ready to return home to Death City. However, Maka's new ability to sense wavelengths picks up on a technician and their weapon along with a massive cluster of human souls. Soul asks whats wrong as she notes that all the human souls disappeared and the technician is still there. She begs Soul to take her there as they arrive at the church. Maka dreads going inside but she vows its her duty to investigate these sort of events.
In the church, we meet Crona as she notes that Maka has arrived. Maka demands to know if they are a part of Shibusen, but then the demon blade Ragnarok appears out of Crona's back, shocking the two as Soul turns into his weapon form as the two fight. Back at the academy, Spirit laments on how the nurse isn't in today as he plans to flirt with her. Stein comes in instead as he mocks Spirit on his recent divorce. He demands to know what Stein wants as he is told that the demon weapon has emerged. Back at the church, Maka sees how Ragnarok's soul is overpowering Crona's as the two battle. Maka gets a few hits in only to notice that Crona's blood hardens due to Ragnarok's power inside of her. Maka blocks Crona's attacks with Soul but Crona is able to use Scream Ressonance to vibrate and damage Soul.
Maka falls back as she doesn't want to injure Soul. Soul chastises her since he points out that it is the weapon's duty to protect their technician, but she fails to listen as she continues her attempts to escape. Crona notes that the doors only open one way as she closes in to attack. Maka tries to figure out what to do as Crona slashes at Maka, a fatal attack if not for Soul. Soul intercepts the attack as he is slashed deeply in the abdomen, falling over as he bleeds out. Maka cries over her fallen partner as Crona hovers above her. She goes in to kill Maka but something impales her and pushes her back. Maka notices that the blade is her father as Stein and Spirit bust through the door of the church.
As Maka tends to Soul's wound, Crona overlooks them as she continues to get messages from a witch to go ahead and kill the two. Maka tries to defend Soul, knowing she is not strong enough to beat Crona by herself due to her black blood. However, something pierces Crona and causes her to fly back to the altar in the church. Maka notices immediately that the blade of the scythe in the door looks like her father as Spirit emerges to protect Maka. He assumes that this will make her daughter clamor for her, but she is too busy asking Stein to tend to Soul's massive wound. Stein does what he can as Crona gets back up to fight, claiming she doesn't know how to deal with the man with the scars. The witch uses her manipulation on her as she begins to fight again. Stein and Spirit go back on the attack as Stein is able to use his Soul Wavelength to attack Crona directly without having to go through her black blood.
Thrown outside, Crona is being beaten heavily by the duo while Maka watches over Soul. She notices the power level of the two fighters as something goes wrong with the black blood inside of Crona, causing it to overload and for her to pass out. Stein plans to bring her back to Shibusen, but the witch from above releases her Soul Protect to claim her experiment. The group immediately notices the revalation of the witch and prepare to fight her. She is in no mood to fight though as black snakes emerge from her body to collect her subject, claiming that she will punish Crona when they return to her lair. Leaving in haste, Stein collects Soul to operate on his wound.
Back at Shibusen, Maka worries as she waits patiently outside of the operating room. She blames herself for not being able to protect Soul, despite the fact he was willing to sacrifice himself for her. Spirit comes by to try and cheer her up, but his attempts fail as she gets even more depressed. Stein emerges from the infirmary to inform Maka that Soul will be fine as she goes in to see him. Spirit notices that Stein is worried even though he doesn't show it. But being his former partner, he can tell something is wrong. Stein informs him that the black blood from the sword Ragnarok mixed in with Soul's blood and the consequences of this are unknown.
In the hospital room, Maka worries over Soul as Black Star and Tsubaki come in to see him as well, the former over-reacting and shaking an unconscious Soul. The regular Shibusen doctor returns from her trip to see the commotion and claims to be glad that Soul is fine. What no one knows though is that the doctor is actually the witch Medusa who they encountered in Italy. The volume comes to a close as Medusa muses about the experiments she will run on Soul and Maka to test the black blood.