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Scouring the planet SR388 to exterminate the Metroid species proved to be a daunting task for Samus as she discovered that the Metroids were capable of detaching from its standard body in order to evolve into a stronger form. Despite this ordeal, she was able to overcome every Metroid that she encountered on the planet and was also successful in destroying the Metroid Queen. It appeared that once again Samus had accomplished her assigned mission and so she began to venture back to her ship to return home. However, on her way back she encountered a Metroid egg which immediately hatched and resulted in a newly born Metroid larva. The Metroid larva's first vision was the sight of Samus and so it immediately bonded with her as it determined that Samus was its mother. While it was Samus's duty to destroy every Metroid on the planet, she could not find it in her heart to destroy the baby Metroid and instead brought it back with her to the Galactic Federation Space Colony for scientists to conduct further research on the species.
During their research, scientists have made a remarkable discovery about the Metroid's energy-producing capabilities and how it could be used to benefit the world. Opinions of the Metroid species slowly began to sway away from the original thought of its kind existing simply to wreak havoc on the planets that it inhabits. With the Metroid in captivity, the galaxy appeared to be free of any further threats. Suddenly, Samus receives an emergency distress call from the Galactic Federation about trouble within the Space Science Academy. Once she arrived, she immediately ventured into the research lab. While the area was vacant from any Galactic Federation members, the Metroid larva was still in captivity and appeared to be unharmed. Without warning, a large figure then slowly appears and it is identified as the creature known as Ridley who Samus had battled during her past mission on the planet Zebes. Ridley's sole mission was to abduct the Metroid larva. While Samus attempted to stop Ridley, she was unsuccessful as Ridley quickly returns to newly rebuilt planet Zebes.
Realizing that the space pirates are once again attempting to use the Metroids as a weapon, she quickly travels to the planet Zebes in an attempt to foil their plans and to save the Metroid larva.
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