This world has gone through many Dusks, and is slowly nearing its end. Within this world, in the western reaches of the "Land of Dusk," there was a nation that prospered thanks to its use of alchemy. There, in order to survive the eventual arrival of the "Dusk End," the people devoted their efforts to rediscover and recreate lost alchemic technologies. Rediscovered technology from the past era was gathered in the alchemy research city known as "Central," where research was conducted on how to halt the advance of the twilight. One of the heroes is a young man who researched alchemy in Central, the other a girl living in a small town on the frontier. This girl's name is Escha. In the process of using her knowledge of ancient alchemy to help others, she was assigned to the Development Department. The young man's name is Logy. Having learned the newest alchemic techniques in Central, he requested a transfer to this understaffed town to make use of his abilities, and meets Escha when he is assigned to the Development Department as well. The two make a promise to use their alchemy together, and bring success to the Development Department.

Shou Zama is an ordinary 18-year-old from Tokyo who finds himself summoned to the medieval fantasy world of Byston Well. Upon arrival, he is put into service under the ambitious lord Drake Luft, who seeks to greatly expand his power. Those like Shou who come from "Upper Earth" possess strong aura power and are ordered to pilot "Aura Battlers," insectoid mecha designed by a man named Shot Weapon, who also came from Upper Earth. However, Shou's alliances quickly change when he meets Marvel Frozen, a young woman who has decided to rebel against Drake's political agenda. As he realizes the lord's true intentions, the boy chooses to join the fight against Drake and team up with Neal Given, who leads the resistance movement. The resistance isn't alone—Riml, daughter of their enemy and Neal's secret love, aids their efforts, hoping to escape from her father's clutches. As Shou finds himself fighting alongside his new comrades, they put their lives on the line to prevent the villainous Drake from taking over Byston Well before it's too late.

The stage is the close of the Edo period, an age when, not unlike our own time, both natural and man-made disasters left chaos in their wake. Manjiro makes a living helping the people of the troubled capital city, but behind the scenes, he also works in secret to take back precious belongings stolen from the people by unjust political powers and conspiratorial menaces. The people call him "Get-backer Roman."

Despite the kaleidoscopic magic ingrained in everyday life, Hitomi Tsukishiro's monochrome world is deprived of emotion and feeling. On a night as black and white as any other, amidst the fireworks spreading across the sky, Hitomi's grandmother Kohaku conjures a spell, for which she has been harnessing the moon's light for 60 years, to send Hitomi back in time to the year 2018 when Kohaku was in high school. Hitomi's mission seems unclear, but her grandmother assures her that she will know when she gets there. Following a trip through time aboard a train driven by a strange yellow creature, Hitomi finds herself in stoic artist Yuito Aoi's room, and his drawings flood her world with color. What is Hitomi's purpose there, and why do Yuito's drawings return such breathtaking color to her drab world?