A mysterious meteor has struck Sweet Apple Acres, one of multiple spots all over Equestria. At first, everypony thought it was harmless. But then green crystals started growing from the crater, leeching all the minerals and nutrients from the soil.

And everypony that came near or touched it started mutating or dying. And the alien substance continued to grow and expand, and nothing seems able to stop it.

An unknown figure then emerges: a maneless red pony with a black mustache and goatee, and an equally mysterious cutie mark of a scorpion tail inside a triangle, known only as Kane. He says the new substance is the harbinger of a new age, and all ponies should embrace it (carefully, of course), under the Ponyhood of Nod, an ancient and secret organization.

The Princesses Celestia and Luna disagree, and the Equestria Defense Initiative (EDI) is founded, and prepares to stop the Ponyhood, as well as the alien substance, which is quickly growing out of control.

Equestria has just entered the Tiberium Era. The question is: will they survive it?