Fluttershy, after the apparent loss of her woodland family, especially Angel, finds herself in an apocalyptic Equestria, leaving her in a state of emotional scarring, rejection and egoism.
With only a fraction of the world's population unaffected by the magic based infection, which prevents almost every sort of magic from being usable, she hides herself in one of the few save zones, to be precise, in Manehatten.
Working as a courier, alongside her close friend Rarity, she finds herself being dragged into a mission, where there is no return. Send by Twilight Sparkle, she is tasked with bringing the young dragon Spike to a distant place, where the remainders of the Royal Guard might be, as he seems to be immune to the infection and is possibly the key for a cure.
Throughout their journey, they must overcome many obstacles, enemies and themselves, to reach their goal in a desolate, hating world of misery, despair and death, in which both must face past friends and past enemies.
Even though their goal is clear, their path and result may not be what it seems to be, and soon, Fluttershy finds herself in a moral dilemma, in which she tries to prevent her last spark of ponyty from dying out, like everything else in her heart.
(Key-plotelements may be spoilers, though they are generally altered)