In her life, Fluttershy was always kind to her animals, her friends, and even wild animals. On an afternoon, she realizes her life could use a little more excitement, instead of living inside her wood cottage most of the day. Fluttershy writes a letter to Twilight Sparkle and the unicorn sends her a computer, and tells Fluttershy about a popular game known as "Minecraft", and tells the pegasus to try it for herself.

However from a wish she made, Fluttershy finds herself transported into the game that she once thought was peaceful. The yellow pegasus eventually finds herself in a nearby village in critical condition, only wondering on how she survived a potentially lethal creeper attack and who or what saved her. She soon meets Will the blacksmith, her savior, and together they start to live together in the village. Yet, how long do these relationships last when mysterious events start in the village, a baby is taken away, and monsters attack at every turn? Fluttershy once thought the game was meant to be peaceful, and travels with Will to the ends of the digital terrain to find a way to get back to her own world.