Now that Akari Mizunashi is a Prima Undine and head of the Aria Company with her own apprentice, Ai Aino, she can't help but reminisce about her time as a Single. She has new responsibilities and much less time on her hands, but these changes bring with them new forms of miracles that Neo Venezia can give. Growing up into new roles is hard, but Akari can always count on the friends she's made on Aqua in times of need.

Akari Mizunashi dreams of life after attaining her goal of becoming a Prima Undine, but upon waking realizes that she might not actually have the confidence to run Aria Company on her own. Wary of the future, she seeks advice from her mentor Alicia Florence—one of the three great "Water Fairies" of Neo-Venezia. Much to Akari's surprise, Alicia reveals her own struggles of the past, but also shares the steps she took in overcoming her self-doubt of running the company and taking on an apprentice. Finding solace in her teacher's words, Akari prepares to embrace whatever trials she must overcome on her path toward achieving her dreams.

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.

More than twenty years ago, an evil summoner committed "Great Summon". One third of human beings were killed, and devils and monsters invaded the Earth. One day, a painter, Tamura Fukutaro, moves into an apartment house called "Ashiaraiyashiki" and gets involved in the troubles of his non-human neighbors. It's the beginning of a severe battle among gods, devils and the ruler "The Central".