The developers have included a constructive and extensive story that help develops the story of Samus Aran and the many different themes, species, and antagonists of the series, along with giving new worlds to explore and learn about. If the player wishes, he or she is given the chance to learn more about every aspect of the plot by scanning the copious objects in the game.
In the beginning, Samus Aran will land on the Frigate Orpheon, responding to a distress call she received. Once she is ejected from her ship, she explores the inside where she finds that the entire crew has been ambushed by a mutated parasite that became corrupted through the Space Pirate's experiments with Phazon, a dangerous and powerful substance that is destroyed in the final installment of the series, Metroid Prime 3: Corruption for the Wii.
After fighting and ultimately killing the mutated beast, who's name is the Parasite Queen, the boss falls into the ship's reactor, thus making it explode within a few minutes. Samus escapes, though she looses all of her weapons through an electrical surge that resulted in the destruction. This is when she spots Meta Ridley (Ridley's reconstructed form), who flies off to Tallon IV. Samus makes an appropriate decision and follows him onto the planet.
