Plot revolves around starting life on a revolutionary planet Elysia once overruled by space pirates.

The current inhabitants call the planet Skyloft. It is a time of industrial advancement. Samus Aran was awarded captain of the federation force. She & her squad help gather materials from other planets to provide for the Skyloft's growth. She enters Brinstar since it contains material to sustain colonization on Skyloft. Her team is made up of an elite group of human soldiers, Sargent Jason McCloud, Rovio Hare, Fi Lombardi, & Mamu Kinopio. The team must separate in order to locate as much resources as possible. Along the way Samus encounters a queen Metroid who had evolved into a new species. The new Metroid is called didongoid.

Game starts in the battle with the didongoid. To take it out, Samus feeds the creature bombs. Samus explores even further to find that there are space pirates here who are growing snouts. These creatures are called moblights. In fact, every creature here has evolved from one shape or another. One particular being has evaluated to great power. The Sheikah Mother Brain. With a tear of lite, this creature can provide cities with countless energy. It is up to Samus to defeat Sheikah Brain and harness her ultimate energy to power the new city.