The story features Homura Akemi (Puella Magi Madoka Magica) as the main character, and is primarily told through her point of view. Every character that appears in Malign Quarantine is confirmed to make an appearance. In addition, other characters not present in the game also make appearances, and are described to be due to "timeline anomalies".
- Homura Akemi (Puella Magi Madoka Magica) is the main protagonist of the story. Traversing multiple timelines, she fights to save the other characters from the Malign Virus.
- Death the Kid (Soul Eater), or Kidd, is an antagonist in the story. Aside from his brief appearances in Chapter 1, Homura reveals that he is the one who destroys the world.
- Kyoko Sakura (Puella Magi Madoka Magica) is a Magical Girl, and a friend of Homura. She often works alongside Mami in fighting Wraiths, and is known for her love of eating, as she is always seen to be eating a snack.
- Mami Tomoe (Puella Magi Madoka Magica) is also a Magical Girl, and Homura's rival in Wraith hunting. She tends to keep her emotions bundled within herself, only expressing gratitude and positivity externally.
- Kyubey (Puella Magi Madoka Magica), or Incubator, is a cat-like extraterrestrial that is able to grant girls with enough potential a single wish. His alien race "powers the universe". He acts like the chief of the Magical Girls, and often tags along with them when not looking for candidates.
- Patty and Liz Thompson (Soul Eater) are twin girls with the ability to transform into pistols. Patty is shown to be enthusiastic and childish, while Liz the opposite. They are often seen with Death the Kid.
In a dark, ruined city, a girl with long black hair and a white , a teenager with a dark, black jacket and brown hair and a tall, red head stand facing a girl in a black combat skirt and emitting a purple aura.
"Do you really have to do this?" the red head - Alpha - calls out to her. "Come on Ruby! You can fight it!"
The girl, Ruby Rose, shows him a crooked smile. The purple markings that cut through her skin, glowing brightly.
The girl throws her large red scythe at the red head, impaling him in the chest like a dagger. "Oh my. That looks like it hurt." she teases, her voice deeper and more gravelly.
The brown-haired man in a dark jacket pulls the scythe from the chest of his friend. Checking to see if the man is still alive, he quickly turns to the girl. "Homura. You can fix this."
Tears stream down the girl's cheeks. Staring at the burnt body of her best friend, who now lies forgotten behind the other girl, she slowly nods. "I can."
"Good. I believe in you." he transforms the scythe into a shotgun. "Now, save us. Stop this before it even happened. I'll hold her off."
Homura slowly stands up, her legs quaking. "Okay. Thank you, Umbra."
"Any time." he says, before shooting a blast at Ruby.
The world around Homura slowly starts to disintegrate, as blue light starts to scrape away at the reality around her.
The final thing she sees as she warps out of existence are the painful eyes of Umbra, closing as a bullet strikes his forehead, piercing the quartz-like stone that is his skull.
Then, the blue vortex of memories suffocates the girl that is Homura. Wrapping around her like her own personal cocoon.
If only they knew.... she thinks, as the bright light of time encompasses her.
A flash of white light, then I open my eyes. My black hair, long and sleek, glides over my eyes as I sit up in my bed.
"Let's try this again." I mutter, jumping out of bed. I land on my feet, and look up at my scaled model of Walupurgis. The nightmare witch, the reason for my despair.
I reach for my drawer, and quickly dress in my school uniform: a black and white-plaid miniskirt with long black tights below a beige dress-shirt.
I reach for my red ribbon: the red ribbon that Madoka gave me before she made her wish.
The only remainder I have of her.
Tying it around my head, I quickly walk out of my house and towards the school, where the other Magical Girls study.
But instead of studying, I'm trying to do something else.
I race through the school's garden, before racing up the steps of Mitakihara Middle School. I need to find that strange man. I think, jumping up the stairs.
I hear two girls talking around the corner that I plan to turn, followed by his voice.
"Don't you two know anything!?" he says, his voice angered, yet calm at the same time.
I peak around the side of the golden wall, expecting to see him and the two weird girls - the "Thompson Sisters" or whatever - that follow him where he goes.
Instead, I see him holding two pistols.
"Come on. We have to hurry." he says in a loud whisper.
This guy's a nut.
Then, the unthinkable happens. A girl's voice comes from one of the guns he is holding. "Sorry about that, Kidd."
Chikushō! I think, backing up behind the wall as the man named "Kidd" runs past, not noticing me. What is with those pistols of his?
The school bell rings, piercing my ears, as I watch the strange, black haired man disappear into the distance. Yatsu, I mentally say to him, before turning back around to the entrance to the school.
The three beats for the end of the school day sound over the PA. I sigh as I slowly walk out of the classroom, behind the red-haired girl Kyoko.
Kyoko, like I, is a Magical Girl. A girl originally given powers to hunt witches, now forced by the alien Incubators to fight the Wraiths in order to power the universe.
Frankly, I think they're just perverts who like to watch [young] girls fight.
I turn on my heels as I walk out of the school, seeing the black haired kid with the three white stripes on his head barrelling down the pathway.
His pistols, nor the Thompson Sisters, are with him. Odd.
I shake my head, before slowly following him. I can't believe it's this yatsu who destroys the world.
As the world around me slowly comes to a halt, I transform into my Magical Girl uniform, and stride the path of truth toward my target.
Looks like no Wraith hunting for me today.
I sneak behind the large water fountain that rests inset in the golden pathway. The sun now hovers over the crest of trees, painting the sky a beautiful gold colour - the colour of Mami's hair. Like a wolf stalking it's prey, I am ready to strike should time arrive.
Kidd, or whatever his name may be, finally stops his cautious stepping, and looks around. We're in the school's gardens, dedicated to the founder of the school, Hisao Mitakihara. The golden pathway - which are actually just yellow stones - separates two identical flowerbeds, both sporting symmetrical - or as close to - eyes planted from roses.
As if Mitakihara-san is watching us right now.
"I can't believe it." I hear Kidd say, as he drops to his knees. "This is the most symmetrical place in existence!"
This yatsu is obsessed with symmetry. I realise. That's why he's here.
He swings his arms in an arc, and, with a flash of white light, his two pistols appear in his hands. "That was quick." he mutters.
"That's us. Waiting at Death's door." a feminine voice squeaks, and I can barely make out the words.
But I heard enough.
Did she call him Death? I stumble. Death the Kid.
I think to the school. Two Magical Girls, Kyoko and Mami, said they were going to track a Wraith that appeared right outside the school. And if I am right.......
I spin around, my black hair cocooning my head.
In the first timeline, Mami and Kyoko were killed sometime between the third - two days ago - and the ninth. Their bodies ripped to shreds in the force of an explosion done by the work of - as the news described it - an "elite terrorist faction".
They found a single note at the school: "死 Kid". Some suspected it to be the name of the terrorist group, the Death Kids, while others thought the leader of the faction was to be named Kid, and this was his taunting.
But no one figured out why.
"Are you sure that's where it is?" Death says, a state of anger, confusion and annoyance coating his words. "I don't want to go around blowing up buildings if I don't have to."
"Well," the girl's voice says. Where the chikushō are those voices coming from? "90%. At most."
"Greater than 88%, I guess." he mutters, and I can barely make out the words. He throws his pistols into the air, and they begin to glow white.
Okay, I've seen a lot, but this is still messed up. I think, but I don't take my eyes off of the guns as they slowly morph into human shapes.
In a minute, two blonde girls stand next to Death. Both dressed in jeans with red shirts, they look almost like clones.
"Patty." he snaps, turning to the shorter one. "You got the remote?"
"Here you go, Kidd!!" she says cheerfully. The girl - Patty, I guess - pulls it out of her left pocket: a small, silver cylinder with buttons on both the top and bottom. Perfectly symmetrical I think again.
"Let's get this over with already." the taller girl says, eyeing him cautiously.
"Well excuse me for wanting to saviour this moment!" he snaps at her, getting into her face. As he pulls away, she just sighs.
He pushes the button on top of the cylinder, and immediately, I hear a crash. Spinning around, a column of smoke rises from the school.
I wave my hand, and time slows around me, as I run back towards the school. I run through the flowerbeds; a jungle of the bloodied rose.
I rush up the steps, as I unfreeze time. I sigh, as I run in the front door, another explosion rocking the building.
Teachers, three of them, rush towards me. "Get out of here!" I yell, my voice bouncing off the glass walls that separate our cells.
One knocks me with his shoulder, bumping me into the door's frame. I run inside the building, scouring for more people who may not be able to make it out.
Through one glass wall, I spot a man rushing towards the door, only to be crushed by a piece of the ceiling. A feeling of sadness should come for me, but I feel nothing.
I've suffered hundreds of deaths.
Then, I spot them. Mami, her golden hair bouncing as she sprints toward the exit, and beside he, Kyoko, who has a nikuman stuffed in her mouth.
I take a glance at my Soul Gem. Enough I think, before racing towards the two. Mami spots me, and waves, as a piece of the ceiling falls behind her. "Run!"
Mami and Kyoko both make it to me as the ceiling of the room they were previously in collapses, shattering the walls into large pieces. I grab their arms, and slow time - that takes much less energy than stopping it.
"Thanks for the save." Mami says with a smile.
"No problem." I say, turning to Kyoko, as she finishes the nikuman before grabbing another one from her pocket. "We should probably get going."
We run back towards the main entrance, and I notice teachers, and some students, crushed and dying under pieces of the ceiling or stabbed by the shards of glass that made up the walls. Blood stains walls, and the floor. It's like a horror movie.
We rush out of the school as time speeds up around us. I see through the other entrances, that people managed to escape, while some jump from the roof onto nearby trees. At least they're resourceful.
We stand and watch the building collapse slowly in on itself, and it's only when Kyoko offers me a taiyaki do I realise that I am not paying attention to the building, but I am looking for Death.
"Kyubey won't be happy about the fact that we let that Wraith get away." Mami says quietly, before she bites into her own taiyaki.
I take the fish-shaped treat with a nod, and bite into the pancake. The red azuki bean filling reflects the sunlight, and looks like blood. Very fitting.
I take another bite of the taiyaki, and begin to turn away from the school, when I spot him: a boy dressed in all black. At his side, the two blondes from the garden. On his face, a crooked smile.
He says something with a nod, and the girls transform back into pistols. The silver pistols shine an orange colour from the setting sun, as picks them up.
Then he does something I don't expect: he aims them at me.