You are Eli , a solitary electron in our universe.
As predicted by humans a long time ago in a galaxy far, far away the universe is coming to an end in the big freeze. More and more stars and entire galaxies are turning into black holes consuming everything in their way. The black holes slowly evaporate by emitting Hawking radiation, leaving a universe consisting of nothing but a cold dark void.
It is up to you, Eli, to rescue the elementary particles and use them to craft the elements of our world and rescue them from our universe. You have to take them through rifts in space time to a safe parallel universe, preserving them from extinction.
Journeying through the game you will rescue your friends Pomi, the proton, and Noemi, the neutron, thereafter you can chose to play as these characters as well.