When 14-year-old middle-schooler Tsugumi Harudori discovers she is a weapon, she flies to America to enroll at DWMA. There, she meets the absent-minded Meme Tatane and the patrician Anya Hepburn, both of whom are meisters that are also new enrollees.

Fellow student Eternal Feather shows Tsugumi, Meme and Anya around the girls' dorm, and they meet some of the residents there. By the next morning, all three had lost their allowance, and thus had to take part-time jobs at a café named "Deathbucks."

Eternal Feather reveals more about Kim's history, as well as the origin of her name. A new threat, known as "Traitor," menaces the students of DWMA, and Sid sends Clay and Akane to scare them off. Anya feels left out when she misses her turn with Tsugumi.

After a nightmare, Tsugumi wonders why the meisters choose to come to DWMA. She spends some time talking to Akane, who asks her to be his girlfriend, only to say he was joking. The class takes their physical fitness exams, where both Meme and Anya excel.

After dreaming about Kim, Jacqueline is bothered by feelings of attraction for her. Kim leads the girls in a pool-cleaning job, and after she takes most of the pay, they help Jacqueline try to win Kim over, while learning about her mysterious background.

Tsugumi and the others get a bad impression from the Thompson sisters, Liz and Patty, who are working at Deathbucks whilst on probation, having spent most of their childhood living on the streets of Brooklyn. When they run into the sisters later that day, Anya prepares to stand against them with Tsugumi, but is outmatched by their ability to both transform into pistols. Whilst Anya and Meme avoid going to the café, Tsugumi keeps going there every day in the hopes of standing up to the sisters and ordering a pilaf. When one of the customers gets upset with Patty for her rude service, Liz attempts to punch him but Tsugumi steps in and takes the hit instead.

Akane and Clay report to Sid that they suspect the culprit behind the Traitor incidents to be a witch named Shaula Gorgon. Meanwhile, Tsugumi and the others get together for a study session at Deathbucks, helping out when the place gets busier, even if only for a brief moment. The next day, the girls check out the Death Bazaar flea market, where Maka and Soul are running a stand together. Whilst taking a break from her own stand, Eternal Feather purchases a strange scorpion shaped ring from a mysterious woman, who turns out to be Shaula, who uses the ring to put Eternal Feather under her control and make her a Traitor. As Eternal Feather starts attacking innocent bystanders as a result, Maka and Soul step in to try and bring her under control. Feeling Eternal Feather would be outmatched by the EAT pair, Shaula commands her to kill herself, causing her to bring her blade against her own neck.

Whilst Akane and Clay interview Maka and Soul about the incident, Tsugumi and the others are relieved to find Eternal Feather has survived thanks to the efforts of Dr. Franken Stein, though are none too pleased with his pranks. As Eternal Feather steadily recovers from her injuries, Stein reports his findings to Sid, suggesting she was put under mind control by magic. A few days later, after Eternal Feather is discharged, Jacqueline feels downhearted after Kim suddenly tells her they should break up. That evening, Anya and Meme scold Tsugumi for lacking the resolve to settle on a meister partner, telling her she needs to make her decision by October 31st, Halloween.

A series of tales that take place whilst the girls are growing pumpkins for Halloween. During the night, Tsugumi and Anya have to deal with Meme's unique sleepwalking, which proves to be a fearsome fighting style. On another day, Meme wakes up with a bag full of cash, a sloth, and a missing eyebrow, with no recollection of what led her to this bizarre situation. As Meme's investigation continues to leave her with more questions, she eventually finds the sloth's owner and remembers what happened the day before. Later, Tsugumi finds a bat and catcher's glove and decides to teach Anya and Meme how to play baseball, becoming a bit too invested in it. As Halloween nears and the girls harvest the results of their growing, Tsugumi worries about the decision she will have to make whilst Shaula prepares to make her move.

Tsugumi becomes upset when she receives a letter from her mother informing her that her dog, Pochi, had gotten involved in an accident, and ends up lashing out at Meme for forgetting things so easily. That night, Tsugumi and Anya follow Meme during one of her sleepwalks, winding up at the hidden research room where they are discovered by Akane and Clay. Meme is taking into custody, as Sid believes that her sleepwalking and forgetfulness may be the result of being under Shaula's hypnosis. As Tsugumi and Anya become conflicted on what to do, they receive a message from Meme asking them to come see her. However, when they break her out, she is revealed to have been possessed by Shaula and escapes. Sid chases after Shaula, who has possessed some of his men, but is outsmarted by her and found dead by the time Tsugumi and the others arrive. Later on, Akane and Clay reveal they were hired as bodyguards for Anya, who is revealed to be a princess named Anastasia Yngling, ordered with escorting her back home should anything happen to Sid, leaving Tsugumi stunned.

Whilst the rest of Death City celebrate Halloween with a Battle Festival amongst the EAT students, Kim and Jacqueline are tasked with watching over Tsugumi, who had been grounded for her actions. Meanwhile, as Akane and Clay escort Anya towards the airport, the city is suddenly overrun by NOT students turned into Traitors, which the EAT students have to fend off. As Tsugumi states her belief that Anya won't leave the city, mentioning the feelings she sensed from her, Jacqueline, sensing what Tsugumi may be going through, has Kim heal her injuries and lets her go off to help her friends. Hitching a ride with Liz and Patty, Tsugumi reunites with Anya, the two resolving to rescue Meme and managing to perform a Soul Resonance, which gives Tsugumi's halberd form wings. Sensing the two's bonds, Akane directs them towards Stein, who admires their resolve and gives them an antidote made from Meme's blood. Following a messenger bat, Tsugumi and Anya soon arrive at the top of a bell tower, where Shaula and Meme await.

Having spread out Traitors across Death City, Shaula unleashes her magic, making the Traitors more powerful whilst also ordering some of them to kill themselves as she sees fit. Shaula then sends Meme to kill Tsugumi and Anya, with Anya attempting to subdue her to give Tsugumi the chance to administer the antidote. Overcoming her fears, Tsugumi manages to break open Meme's guard and administer the antidote via a kiss. Whilst it doesn't appear to work at first, Tsugumi risks herself to get Meme to remember the times they've spent together, managing to perform a Soul Resonance with her and break her free from Shaula's mind control. Tsugumi then makes the decision to make both Anya and Meme her official partners, believing the three of them can resonate together. Using the remnants of Meme's link to track down Shaula, the girls perform a three-way Soul Resonance to bring out Tsugumi's true form, combining all of their strengths to defeat Shaula, returning all of the infect students back to normal. Some time later, after Anya sorts out some royal business and Meme gets a medial check-up, the two return back to Tsugumi, who has been studying hard whilst waiting for her partners.