Samus Aran makes her way deep into the catacomb-like geography of Tallon IV.
- - - Mission File 01312 - - -
Secret Space Pirate Outpost
After total loss of the Zebes base as well as massive casualities to their regime, the Space Pirates had retreated to recover from their losses. Their plans to use the Metroids were far from over. Samus Aran tracked the Space PIrates to an orbiting station over the planet Tallon IV. By the time Samus had reached the station it was in total disrepair due to specimen contamination. The pirates were conducting experiments with various lifeforms recovered from Zebes as well as Tallon IV in an effort to genetically engineer them with a compound known as "Phazon". Upon destruction of the station, Samus came face to face with Ridley, one of the Mother Brains's commander-in-chiefs which she had defeated on planet Zebes. Not only was Ridley represent, but he was also fused with the pirates new Meta technology.

This revelation could only mean one thing: the Pirates had means of which to revive their fallen leaders. Following Ridley to Tallon IV''s surface, Samus was determined to find out what the Space Pirates were planning. Her determination paid off as she uncovered a new Metroid breeding program on the planet's surface as well as extenisve underground mines for which the pirates were obtaining all their Phazon from. She had also discovered the exsistance of plans to re-engineer the planet Zebes. Battling her way through the Space Pirate defenses, she also discovered samples of the Space Pirate's latest creations: Eltie Space PIrates, pirates which had been genetically enhanced with the Phazon mutagen.

Already in the prototype phases of development, she battled with these frightenlingly powerful creatures to eventually come face to face with Ridley once again. After defeating Ridley, Samus traveled to the heart of the Phazon source only to reveal the presence of a new horror, the Metroid Prime. It seemed the Metroid Prime had been the source of the Phazon Upon defeating the Metroid Prime, Samus narrowly escaped, once again leaving the Space PIrate research facility in ruins.