Ignoring other events at the end of the anime, Shibusen defeats the Witch organization, Arachnophobia. However, in the process of doing so, they lose track of their two most potent enemies--the Witch Medusa and the Kishin Asura. Medusa takes the remnants of Arachnophobia and reforms them under a new, nameless, and thus harder to root out, banner. Her first maneuvers are a couple of swift strikes against a recovering Shibusen that accomplish two very important goals. One, the apparent death of Shinigami-sama, ruler of Death City, and two, the kidnapping of Marie Mjolnir.
It is June 2009, and Shibusen finds itself suddenly without its leader and both primary defenses against Asura’s growing world-wide Madness. Without options, the ascending ruler, Death the Kid, young and inexperienced, uses the Demon Tool ‘BREW’ to make a desperate wish: Rescue Death City and stop the waves of Madness from overtaking the world. With powers unknown and mysterious to all save the legendary Eibon, creator of ‘BREW,’ the Demon Tool summons in strangers from other worlds and effectively traps them -- for the ‘BREW’ can only fulfil one wish at a time.
Here is where the game begins.
Shibusen and Death City scramble to accommodate their new ‘Guests.’ By way of apology, measures are implemented to provide food and lodging for the strangers. Upon discovering the strangers’ strong potential as either ‘Weapons’ or ‘Meisters,’ Shibusen establishes training programs and classes and writes up contracts of enlistment that ask for a guarantee of loyalty from Guests before training can be dispensed. Unfortunately, resentment among the new arrivals is high, and only a few agree to be ‘dogs’ to Shibusen and its unorthodox war.
Among the new arrivals is Tohru Adachi, a narcissistic killer from one of the many versions of Japan. As Asura’s influence on the world grows and Madness waves become less subtle, Adachi begins a murdering spree throughout Death City. He uses the waterways to evade capture and travel undetected; over thirty Guests and D.C. residents fall victim to his lust for power. Adachi devours their souls and walks the path of the Kishin, granting him new and terrifying abilities--the most potent of which is the power to generate a yellow fog that gives life to its victims’ unwanted negative desires. However, the power he ingests soon becomes unstable: the murderer grows into a giant lumbering mass of tentacles and attacks on instinct. Though he causes great damage throughout the city, Shibusen and the Guests work together to successfully defeat this formidable foe. Adachi is caged, and his energy is channelled to produce a shield around the city to prevent future cases of Madness-induced rampage.
Another Guest, Jonathan Crane, also becomes a potential threat when he utilizes disguise and subterfuge to administer an experimental Fear-Madness-inducing serum on select members of the Guest community. Patrols are created by the Guests, but Crane, unlike Adachi, hides in plain sight amongst the Guests, charming them with his true identity and using them as guinea pigs with his alter ego, the Scarecrow. Unfortunately for Crane, his identity is quickly made public knowledge by a fellow Guest, and he becomes the first trophy of the Guest-created Detective Agency.
Perhaps in recognition of positive Guest initiatives during these two cases, Shibusen removes the need for a contract. All Guests are now permitted to learn their new Weapon and Meister powers under Shibusen’s careful and expert guidance.
Saving Marie Mjolnir
Realizing how vulnerable they are to Asura’s Madness, Shibusen makes every effort to discover the whereabouts of Marie Mjolnir. With human resources stretched so thinly just keeping the Guests in line and occupied, outside assessor Joe Butattake volunteers to find her. His investigation leads to NORAD in Colorado, now a den of militant kishin being controlled by a group of Medusa’s Witches. Although Joe manages to send a detailed report of his findings to Shibusen, the message he sends is abruptly cut-off by what is perceived as an enemy attack. Shibusen mobilizes the Guests for their first mission outside of the confines of Death City, reacquiring Marie, but losing Joe.
Although quickly contained, Jonathon Crane is recognized by Medusa as a fellow scientist and potentially valuable asset. While the majority of Death City’s capable combatants are in the field, she orchestrates a prison break for Crane and recruits him into her organization. With Medusa’s resources, Crane is allowed to continue his unethical experiments unimpeded.
Ten Years Later
Sudden, unexplained spikes of worldwide Madness penetrate Shibusen’s new barrier, altering reality within and around Death City. Under the influence of Asura’s Madness, Guests discover their original powers returned, and the resulting rampage leaves the sections of the city in shambles. Using the time-altering powers of Miranda Lotto, four Guests are sent far into the future where they find a world covered in Madness, ruled by Witches, and devoid of Shibusen.
The four Guests--Miranda Lotto, Winry Rockbell, Kanda Yuu, and Yuuri Shibuya--join with the renegade remnants of Shibusen under Death City and in the nearby mountains of Death Valley. While among the Guests of the future, they learn that Shibusen’s losses began with the assassination of Spirit Albarn at the hands of Chupacabra hostesses Risa and Arisa, and resolve to go back to their own time to prevent the terrible chain of events.
Meanwhile, back in the present, the Madness Wave subsides and life returns to normal until a wave of kidnappings causes panic in the city. Using this circumstance and the past success of Guest-organized patrols as impetus, Roy Mustang pushes forth the proposal to form the Death City Office of General Security (The Watch).
In the mean time, kidnappings have been happening in Death City, with nothing but handfuls of sand to mark the site of the kidnapping to help them as a clue. The guests combine their efforts to put up a group to patrol the streets and a surveillance system to keep watch of the public areas of the city (the Watch and the Agency respectively). Giriko, the enchanter tasked to acquire residents and guests from Death City, becomes impatient and sends his sand constructs to invade the city for a large sweep of victims.
Where Eagles Dare
The guests who have ended up in the future bring information with them regarding the whereabouts of the kidnapped guests and residences. With this information and Shibusen’s own scouts, they manage to pinpoint where the kidnapees have been taken and prepare for a rescue operation to retrieve the victims and destroy this factory. The factory is heavily guarded by kishin eggs, golems under Giriko’s control, and Giriko himself.
The mission is successful, though the agents find that to their horror, all of the residents have died in the brutal experiments conducted on them and that only the guest victims have managed to survive, albeit with several modifications to them. Using the science brought by one guest, Angelika Einstürzen, the witches have done the impossible: the guest victims have been forced to contain the Sway of Magic, nominally making them akin to a lesser witch, with abilities or animal forms to go with the change. Shibusen dubs them as the Hexed and assigns an agent with Calming Wavelength to watch over them in the clinic. Stein and Spirit eliminate Arisa, while several guests also manage to kill Crane during the event.
If there is something this event has done, it is to emphasize the identity of the real enemies in the minds of the guests.
All Hallow’s Eve
Peace reigns in Death City for a while and everyone takes the opportunity to breath. Shibusen releases more missions for the public, the Watch gains members, more people SUDDENLY COMES IN via BREW, and all is well. Well enough for people to go out to a massive cruise Shibusen holds to introduce the guests more to this world as a sort of cultural event. During this cruise, Medusa’s snakes get into some of the guests and lie there in wait.
Halloween happens, people are still in relaxed mode and decide to party in costume and all that. Witching Hour comes, the snakes take control of their hosts, and the city receives alarms for guests rampaging through the streets. On top of all this, Giriko, Free, and Eruka attack the city and make straight for Shibusen. Divided, distracted, and confused, the guests are unable to stop the three from stealing Adachi from the Shibusen chambers, removing the barrier that protected them from Madness and allowing it to come rolling into the city. The Madness exacerbates the problem, and a hundred people die before Shibusen and the guests manage to get things under control.
Death the Kid takes the position of Adachi to keep the barrier up, but it is not as powerful as before and can only keep the Madness out. Sarah Kerrigan of the guests takes effort to track down Giriko, Free, and Eruka, and return to report about her findinds. Shibusen sends their scouts to investigate the matter, but they are discovered because of their powerful souls and eradicated before they can complete their mission. Mifune returns home from attempting a reconnaisance with the scounts to report about the failure, and suggests sending guests instead. Kerrigan and Roy Mustang volunteer themselves for the job and Shibusen accepts.
Dawn of the Kishin
Now that the barrier keeping Death City safe is down, Medusa and the witches send an army of kishin eggs to attack the city and test its strength. Fortunately, some of Shibusen’s operatives (Mifune, Leo, Yuuri, Conrad) are able to see the attack approaching the city and Death City is able to prepare for the attack. Swarms of kishin eggs invade the streets but are beaten back by the guests and Shibusen agents.
Later on, everyone discovers that Death City was not the only target of the attack -- New York, Paris, (such and such) also suffered from the attacks, with more devastating results. New York, in particular, loses many of its residents and agents.
Sarah Kerrigan and Roy Mustang return to Death City to report the whereabouts of a witch base -- a second factory -- in Arizona. Shibusen begins preparation for a mission and sends the guests to destroy the factory.
The mission is successful -- more than expected -- and despite some casualty and injury from the fleeing witches, the group has reason to celebrate upon the capture of one witch.
Brightest Sale and Blackest Night
After a period of moderate peace occasionally disrupted by violence among the guests and even a festival to welcome Christmas, a crisis occurs in Europe that shocks the world: several Shibusen bases along the Alps have been raided by enemies unknown and engulfed in black balls of Madness. Kishin numbers are on the rise, Europe is in panic, and Shibusen answers the challenge by calling for reinforcements from its American and Australian counterparts.
Death City responds by sending some of its prime agents to the scene, including volunteers from Death City’s guests. A simultaneous attack by Black Clowns on Lucerne, Linz, and Ravensburg leave West Europe heeling. Lucerne falls in the aftermath of the event, with its refugees running to Linz to escape the black ball.
Meanwhile, the American Board of Industries announce a nation-wide mall sale across all of its member malls. The first day of the sale goes disastrously. With emotions and tempers high because of the crowded malls, the Madness finds easy prey in the nation’s shoppers and riots are reported through all American states. Shibusen agents enter the fray as crowd control, and later to eliminate the resulting kishin eggs from the disturbances.
Shibusen West and East Europe merge to form Shibusen Europe and the agents are sent home for Christmas. Problems for Shibusen Europe double when the European Union threatens to close its funding on Shibusen European operations unless results are found.
A Series of Unfortunate Events
A number of connected investigation missions lead to the discovery of various devices that function as emitters of some sort. Further inquiries by Shibusen to their resident prisoner Witch reveals that the Witches plan on using these prototype emitter towers to cause chaos and unrest in continental Europe. In an urgent mission cobbled together to Europe, Shibusen agents manage to destroy the towers in the nick of time.
The event, while a success, doesn’t bide well for Death City. In retaliation, the Witches plan an intricate raid on the city involving Black Blood in the city’s water reservoir, followed by an attack of Witches and familiars. Their goal is unclear at first, but soon reveals itself as many agents and some civilians are taken by the Witch familiars. Cybele, the Witch prisoner, is also a target of Witch assassination for giving Shibusen the earlier information about the emitters. Enraged at the betrayal, Cybele teams up with Spirit to ward off her would-be murderers. Suffice to say, the assault leaves Death City sorely shaken but relentlessly determined to retrieve its kidnapped comrades.
Meanwhile, the kidnapped victims are taken to a network of caverns in the Grand Canyon and subjected to the manipulations of the Morality Manipulation Machine, which brainwashes them to the Witch side. Those who resists are thrown into a feeding cage -- except they are the feeds, for the fattening of kishin eggs in a pit.
Shibusen launches an ambush two days later and successfully rescues their agents, destroys the machine, and kills two Witches. It’s a happy ending for most, though the victims may think otherwise.