In a flashback episode taking place five years prior to the quest events, Malal travels to Varrigan City to save a kidnapped rookie. Varrigan City is a dangerous place filled with criminals and refugees, augmented humans and rogue magical girls and said to be one of the worst places in the world. Malal literally coerced Kyubey into allowing the mission and refused his support to make use of her own connections.
After a rough trip with Kyubey's teleporter where she had to force herself out of the warp near the end, she arrives in Downtown Varrigan City and is contacted by her support, Xiaomei Baocun from the Seventh Officio, via her suits communication device. She takes cover on a nearby rooftop to avoid any unpleasant surprises and has the disgruntled Xiaomei refresh her memory of the mission target.
She is to find and save a Vindicare recruit named Ekaterina Valnikov who went missing a few months ago, suspected of being abducted by the Tenth, although no evidence for their involvement was found. She was declared deceased a month ago, but Malal refused to give up, stating that finding her is important.
Xiaomei also informs Malal of her local contact, Professor Madaraki The Second from the Thirteenth Officio and her last known whereabouts and how to best reach her. She tells Malal that the evacuation transport will leave in four hours and reminds her to watch out for the Eighth Officio as she is in their territory.
They end the call and Malal gets up to move out, but is interrupted by a group of punks trying to capture and violate her. Malal thinks about talking her way out, but realizes that these punks, unlike the Yakuza clan she belonged to earlier, don't know honor. She swiftly strikes the leader down with her crowbar, terrifying the rest into submission. She demands a motorcycle, and while the gang doesn't have one, one of them offers to show her where he saw a pair of magical girls riding one not long ago. Malal asks about a description, one of them sounds familiar, and has the punk lead the way past gangs looking ready to start a war.
They arrive in the slums and while Malal identifies the bike as Schpeltiger, the vehicle of her acquaintance Nicole Touchdown, the punk cowardly sneaks away. She decides that Nicole would not mind her borrowing the bike and gets on top, but before she can start it, she was the one who set up its touch screen controls, a different magical girl points a knife at her from behind and demands she gets off.
Malal asks for Nicole, the owner of the bike, but is still threatened and does as the girl behind her demands. The girl asks how Malal knows of Nicole, but as the Culexus realizes she is being threatened with a kitchen knife of all things she unleashes her power, disabling the magical girl with overwhelming sickness.
At that moment Nicole shows herself and recognizes Malal right away, calling her by her family name Kaneda. The american non-magical girl makes fun of her "vomit powers" before asking why Malal came to this area and tried to take her bike. She explains to her old friend that she is on an important secret mission with a four hour time limit and wants to borrow the vehicle. They look back on their past and Nicole agrees to lending Schpeltiger, hands Malal the keys and tells her to park it in a safe location with the keys in the lock box once she is done.
They say goodbye and Malal takes the bike to Redline Highway, heading for Asian Town to meet her contact. On the way Xiaomei contacts her again and mentions a distress signal close by, an injured magical girl from the Second Officio calling for help. Malal decides to check it out despite the possibility of a trap and speeds up, finding a magical girl on a badly damaged bike chased by a group of bikers and a roughly constructed tank like vehicle.
She quickly passes by the gang and offers the magical girl a ride, who jumps on Schpeltiger just in time as her own bike explodes right behind them. Seeing this the gang speeds up and Malal releases a bunch of grenades from Nicole's bike, taking the bikers out and damaging the tank enough to slow them down before hitting Schpeltigers booster and leaving the wreckage behind.
Soon after they reach Asian Town and stop to refuel. Malal takes some beer from the bike's integrated mini fridge and offers a drink in honor of the destroyed vehicle, learning that it was the magical girl's first self made bike by the name of Stranger. The girl thanks her savior and introduces herself as Enyo Karasawa, recognizing Malal as a member of the Ninth Officio by her accent.
She explains that she was challenged to a duel to the death and that the Blessed Lady's Champion of the Second Officio's Black Templars is bound to accept even if a trap awaits. She refuses to reveal her opponents identity, but assures that she has a way to leave the city despite loosing her bike and accepts Malal's offer to help if she really needs it. They talk more over their drinks, Malal using a Culexus trick to do so without opening her helmet.
They depart together and Malal drops her off on her way to Great Wall Street where she meets a white haired girl that leads her to the Professor. She introduces herself as Odette Brighton, Warmaster in training of the Seventeenth Officio, and confirms the Professor's identity with a detailed description. In a typical chinese restaurant Malal meets the sickly looking Professor Madaraki who is in an unusually good mood.
After a bit of friendly banter, the Professor takes a big syringe from a suitcase and asks Malal for a blood sample, stating that Xiaomei arranged it as payment for Ekaterina Valnikov's location. The Culexus contacts her support to ask what this is about, and Xiaomei explains that Malal told her to do anything necessary and that she managed to bargain the Professor out of taking live tissue samples instead.
Malal then agrees to giving Madaraki some of her blood who then explains that Valnikov is held in Casino Town to fight in an underground magical girl fighting scene. She also reveals that the Thirteenth Warmaster is keeping Ekaterina captive and conducts experiments on her. She explains that Doktor Emma Strauss is trying to create a symbiosis of magical girl and witch and used Ekaterina as her prototype, breaking her will, body and mind before grafting pieces of witch flesh onto her body and soul gem.
Madaraki also explains that Valnikov most likely doesn't remember Malal and might attack her with the intent to kill. Malal asks for a way to subdue Valnikov long enough to take her outside the city and the Professor supplies her with a hypogun containing a powerful anesthetic that even works on witches.
When Malal demands that she accompanies her, Madaraki refuses, terrified of the place, and explains that she will lead the ousting of Strauss inside her officio instead. To make up for it, she hands Malal her own ID card to enter the lower levels of the Blood God's Arena in Casino City and tells her to look for a young man names Souji who will help her instead. Malal encourages her by saying that this situation is Strauss' fault and she s right to get rid of her.
The Professor then leaves with her pet Xerxes that has been stuck on the ceiling and Odette while Malal heads to Casino town. The huge banner at the Blood God's Arena tells her that Ekaterina's scheduled opponent is none other than Enyo, the Blessed Lady's Champion she helped earlier. Realizing Enyo would not back down, Malal decides to get Ekaterina out before the fight can start and heads towards the staff entrance.
She uses her anti-magic on a magical girl that's singing and dancing in front of two guards to cause a distraction and slips in, exploring the backstage area. Malal decides to take the stairs down, passes several levels of animal pens filled with what looks like test subjects and finds Ekaterina on the lowest level. The russian magical girl is in a bad state, sedated and chained down inside a cage, covered in blood, wires protruding from her head behind a horned black metal visor.
Malal also spots a brown haired man in a lab coat typing on a laptop and identifies him as the Souji Madaraki mentioned. She knocks on the door hard, startling the caffeine filled man enough to send him jumping towards a shotgun near the desk, knocking his face into the furniture. She tells him Madaraki sent her to take Ekaterina away but the man doesn't believe her and clumsily aims his gun. Malal shows him Madaraki's ID, but he calls it fake and tells her to get lost, threatening to shoot her otherwise.
She tries to reason with him, but he mentions that Strauss said somebody would show up with her story. Frustrated Malal uses her magic to disassemble his gun from afar and reassembles in her own hands, stating that she came to steal Ekaterina from the Thirteenth and bring her back to where she was kidnapped from in the first place. Calming down, she returns his gun, telling him that Madaraki would like fixing his arm if he tore it off misusing it. Proving she knows the professor and not shooting him convinces Souji of her intentions enough to help.
Souji explains that he wants Ekaterina out of there and mentions that she kept repeating one word over and over: Malal. Shocked at this, the Culexus turns away for a moment but decides to keep the fact Ekaterina has been calling for her all this time from Souji. The young man deactivates the cage and explains that while unconscious Ekaterina is harmless since Strauss' implants can't turn her into a berserker while her body is disabled. In order to ensure she doesn't activate them during their escape, he suggests keeping Ekaterina heavily sedated.
Malal asks if they could remove the implants right away, but Souji explains that they need a well equipped operation room for the process and have to remove them from both her body and soul gem simultaneously or their link will destroy both when one is removed. He walks over to inject more sedatives, but at that moment Ekaterina's visor starts glowing red and her claws move behind his back.
The Culexus quickly unleashes her power on the russian magical girl, flinging her back as far as the chains allow and making her collapse. Malal tells the confused young man that Ekaterina's visor lit up, which makes him panic as this means she is supposed to go into the fight. Right that moment he notices footsteps approaching and tells Malal to hide from Strauss' personal goons. The Culexus refuses to hide, stating that she found what she came for and will make her way out right now.
Souji calls her plan crazy but figures that he is in trouble anyway, hands Malal his shotgun and tranquilizes Ekaterina. While Malal takes cover Souji distracts the goons until shutting off the lights and diving into cover so the Culexus can kill the six opponents. Malal kills the goons one by one, announcing each kill in a loud voice, saving the leader for last before telling Souji to switch the lights on again.
While Souji prepares Ekaterina for transport, Malal is contacted by Xiaomei who tells her that the evacuation site is compromised by a large number of hostiles. She tells Malal to take Red Highway to the docks and evacuate on the Thirteenth Officio's flagship Rafflesia with Fran Madaraki's help. Malal wants to talk to the Professor herself and tells Xiaomei to look for an alternative escape just in case. Madaraki is glad that Malal decides to accept her help, assures that they will protect her and do all they can to undo what Strauss did to Ekaterina.
Souji wraps Ekaterina in a big poncho to cover most of her body and they head upstairs while Malal convinces herself that people will remember her by what she managed to accomplish instead of what she did for it. Upstairs in the backstage area they notice that battle has started in the arena and realize that Enyo is fighting Nicole Touchdown instead of Ekaterina. Souji tells Malal that her friend will die in this place, but she ensures that Nicole can take care of her own and that they will more likely wear each other out instead of taking lives.
Outside they find a group of guards beheaded by Wendy Cooldown who needs to talk to Malal, Schpeltiger standing ready nearby. Malal points Souji towards the bike and tells him to get himself and Ekaterina into the passenger seat. Wendy mentions that she had a dream about Kaneda Madoka and needs to ask her something.
She explains that she saw her die with a smile, stating that Nicole likes her a lot and would not like her dying at all. She asks Malal if she really plans on getting killed who returns that she is not planning it, but knows her death is a side effect of what she does have planned. She explains that she wants to make it count and asks Wendy not to tell Nicole until after it happened.
Before they can say any more, a new group of goons shows up to give chase and Wendy holds them off while Malal departs with Souji and Ekaterina on Schpeltiger, remembering that she had a dream about the other magical girl's death, too.
While Traveling on Red Line Highway towards the docks and thinking on how to put the broken pieces of Ekaterina's mind back together, Malal's communication is hacked by Emma Strauss. The Doktor compliments her on stealing both her assistant and experiment and wants to negotiate. She offers to spare Malal's life if she returns Ekaterina, threatening to have her killed by the very girl she wants to save after being passed around as a piece of meat throughout the entire town.
Malal spits an insult at Strauss who claims that there is no escape and that she only offers the trade out of the goodness of her heart. She states that she has other experiments, more dangerous than Ekaterina, at her disposal to hunt the Culexus down and demands her surrender again.
Instead of following the topic any further, Malal asks what makes Ekaterina so special to the Thirteenth Warmaster. Strauss explains that she managed to create a perfect synthesis between magical girl and witch, one who retains conscious thought paired with the power of a living nightmare, the first ever Maerorus.
Malal notices a group of armed vehicles quickly approaching from behind and Strauss announces it as the first bounty hunter force. She offers to call them off if Malal stops and tells their leader that she surrenders herself to Strauss' mercy who is instructed to take her group to the Doktor safely after which the Culexus may leave unharmed.
Naturally Malal declines the offer, thanks the Doktor and tells her that she knows for a fact that she doesn't die in Varrigan City. She signals Souji to hold on tight and releases a batch of grenades unto the pursuers before igniting Schpeltiger's booster, darting forward at a speed high enough to push the new bounty hunters joining the hunt aside with air pressure while Strauss screams in rage. Souji shouts something, but the airstream and engine are too loud to hear.
The moment the booster charge runs out, the bounty hunters far off in the distance, Malal notices a place above them and spots the grinning Doktor Strauss at the rear door who sends a bulky, spiked monstrosity with metal cylinders for hands jumping towards them. Estimating the creature's path, Malal waits for the right moment and dodges at the last second, but loses control of Schpeltiger when her opponent grabs the rear end.
The creature is dragged behind while Malal struggles to force the bike back on track, but is eventually thrown off when it tears the back wheel out. The three riders are hurled across the street and the Culexus taps her power to slow Souji's fall, preventing him and Ekaterina from cracking their heads open upon impact. Malal herself hits the road hard, cracking several bones and nearly breaking her spine.
While Malal starts to heal herself, Strauss who is still on the communication line introduces her experiment “Butterfingers” and leaves him to kill her, laughing as the plane flies off. Malal tells Souji to run for the docks and have Madaraki start fixing Ekaterina right away while she takes care of Butterfingers. He refuses at first but complies when she tells him how he is useless in this situation and starts shouting.
The hulking creature charges at Malal, who struggles dodging his attacks with her damaged body before hitting Butterfingers' face with her crowbar, only to confirm her suspicion that it doesn't hurt him. With her weapon bent, she discards it and dashes away. Strauss ridicules her for running, but Malal replies that she is only getting into range.
She holds out her hand and materializes her magical girl weapon, a big rose stalk shaped bow with a blossom bathed in pink flames, a crimson arrow of compressed energy forming in her other hand. Coming to a stop and turning around, Malal draws the invisible string back and takes aim at the charging monster's glowing chest implant. The arrow stops momentarily, growing bigger and hotter, before continuing even faster, a blinding roaring projectile burning right through Butterfingers' midsection and disappearing in the distant sky.
While Strauss screams in shock and rage at the loss of her creation, Malal's bow disappears and she falls to her knees in a sudden wave of nausea and sickness. Removing her helmet just in time to throw up the black blood surging up on the road instead of inside the suit, she hears a familiar voice behind her.
The black haired girl from her dreams, showing an expression of pure hatred, tells her that the contract is killing her and that all of Malal's plans will be for nothing. She spits at the winged apparition who reminds her that she can't save her if her soul is trapped in a gem and screams, asking why Madoka didn't listen to her.
While Malal picks up her helmet again, not showing any reaction, the other girl is incredulous at how she dares to ignore the one who saved her, grabbing the Culexus' shoulder and exclaiming she loves her. When Malal pulls herself free, the apparition starts crying, begging the pink haired girl to at least look at her after she killed so many people and timelines to be together with her.
As the helmet is put back in place, the Animus Speculum's limiter returns from emergency mode to normal and the apparition is gone. Relieved, Malal considers contacting Madaraki to send a transport for herself, Souji and Ekaterina but is interrupted by the sound of an armed vehicle approaching. But instead of bounty hunters Odette Brighton, the magical girl accompanying the Professor earlier, emerges from the top hatch to offer her a ride.
The canadian Eversor helps Malal tie the wrecked Schpeltiger onto the vehicle and feeds her candy while they drive along the road. Upon reaching Souji, the Culexus pretends to be a ganger to mess with him before getting the young man and Ekaterina on board. While the new passengers sleep, Odette explains that Madaraki sent her back into the city halfway to their original destination, to help Malal any way she can. She overheard gangs talking about the bounty and stole the first armed vehicle she could find, smashing her way through any opposition.
The group eventually reaches the harbor and board the Rafflesia. Madaraki welcomes them and orders a group of Medicae to take Ekaterina into a room and prepare for the procedure after ordering the ship's departure.
Souji is allowed to assist after Malal confirms that he was useful in freeing Ekaterina, after which the Professor asks what the Culexus did to him when he would usually never step outside. Madaraki implies seduction, but Malal reminds her that her suit is barely fitting for this kind of thing and explains how Souji cares for Ekaterina enough to trust somebody trying to save her.
Madaraki tells her about how the Officio successfully ousted Emma Strauss and that she was elected as the new Warmaster, now under the title of Chief Director, and promises not to repeat her predecessor's mistakes. She then hands Malal her phone, explaining that Strauss has been calling for hours an that she wants to leave the pleasure of informing the now ex-Warmaster of what happened to the one who made it possible.
Strauss, assuming she is talking to Madaraki, tells her that Malal is approaching the docks and wants the crew to use the ship's cannons to kill her for taking out Butterfingers. Malal enjoys telling the angry woman that she is fired, who only believes her when Madaraki explains that she is no longer fit for the position due to her unethical research methods and abuse of Officio resources. Strauss screams in rage that the Officio belongs to her and how Malal killed Butterfingers, but Fran only replies that the Culexus has treated him more humanely than the Doktor. She also decides to let her live instead of blasting the city into smithereens as an act of mercy before ending the call.
Madaraki then leads Malal to the operation theater to help with Ekaterina's treatment, explaining that she will introduce her to one Misaka later, who wants to meet a Culexus. Malal also decides to write this day's events down in some way and to get a tablet PC back home.