Samus Aran infiltrates the Mother Brain's stronghold on planet Zebes.
The Zebes Incident
A mysterious creature known as "Metroid" was uncovered by a deep space survey team on the planet SR388. The creature was noted as having the ability to draw energy from its prey for it's own consumption. Obtaining samples speciemens, the scientists set back for Galactic Federation Headquarters, only to be ambushed by Space Pirates. The pirates captured their cargo of Metroids, and was believed they were planning to use them for the own purpose of biological weapon. The pirates were tracked to planet Zebes and a regiment of Galactic Federation Marines were sent in. They were met with full fource and completly defeated but not before uncoverin the plans of the pirates. To the horror of all, the true plan of the Space Pirates was revealed: they were breeding the Metroids to unleash upon all Galactic civilization.

It was also learned that the Space Pirates were under the command of a powerfull entity given the codename: Mother Brain. It was decided that outside help would be needed. The emergency order was given to exterminate all Metroids on planet Zebes and to defeat the mechanical life-form Mother Brain. The Galactic Federation employed the services of bounty hunter Samus Aran, who in the past had experience with the Space Pirate menace. Samus defeated the Mother Brain in an intense battle only to find that a self-destruct sequence had been initiated upon zero brain activity from the Mother Brain. Narrowly escaping the blast, the enitre Zebes facility was destroyed, along with masssive cassualities dealt to the Space Pirates.

As Aran was in orbit above Zebes, the arrival of a large Space Pirate armada intercepted her escape and forced her to land back upon Zebes, upon which when she awoke, her power armor had been stripped from her. Armed with only her emergency pistol, she infiltrated the Space Pirate Mothership and regained her powersuit. At full strength, Aran came face to face with one of the Pirates newest innovations: Meta technology. Using this newfound technology, they had created an exact mechanincal copy of Ridley, one of the Mother Brain's top lietenants. Defeating this new menace, Aran once again was faced with the self destruction of the Pirate Mothership. Commendering a Space Pirate attack craft, she escaped the planet for good, leaving the Space Pirate facilities in ruin. Having leads of other possible Space Pirate strongholds, Samus Aran's mission was only beginnning.

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