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With the destruction of the Mother Brain and every Metroid that was on the planet Zebes accomplished by Samus Aran, the space pirates' plans to use the Metroids as a destructive weapon was now demolished. The galaxy was once again free from any immediate threats. Realizing how disastrous the situation could have been if the Metroids were unleashed by the space pirates, the Galactic Federation decided to once again send a research ship to the Metroid's native planet SR388 to ensure that this deadly life form was now extinct to prevent any future threats.
Upon scouring the planet for any signs of Metroids, the Galactic Federation suddenly lost contact with the research crew and a rescue team was immediately dispatched to investigate the situation. The rescue attempt was unsuccessful as communications with the team were also lost upon arrival. Fearing for the worst, the Galactic Federation decided to send a special combat team to fend off any possible threats of dangerous individuals that may be the cause of these activities. However, history would repeat itself as communications with the combat team were also lost upon arrival on the planet SR388.
People began to immediately conclude that the cause for these activities must have been the result of Metroids that are still living within the planet SR388. Once again, everyone feared at the possibility that the Metroids could one day be unleashed onto various planets and wiping out the entire population. After an urgent meeting, members of the Galactic Federation agreed that there was only one solution to the situation: Acquire the aid of Samus to venture into the planet SR388 and abolish the entire Metroid species.
With Samus Aran's new duty in tact, she ventures into the planet SR388 in an attempt to wipe out the Metroids forever.
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