I read about Prime 2's storyline.
After the whole incedent on Tallon IV, Samus is called to a nearby planet where Space Federation agents are stranded. On this planet, she gets caught in the middle of a planetary conflict between dark and light that has been going on for millenia. The citizens of the light half of the planet call on Samus to help them defeat the growing power of the dark half (due to discovery of Phazon no less). Samus has to go deep into the depths of the planet to save her comrades while defeating space pirates who are using the phazon to multiply the power of the planet's darkest creatures. On top of all that, she has to face a powerful recurring foe...an X mutant clone of Samus infused with Phazon.