She will be sent back to Zebes to eradicate the Metroids, creatures created by the Chozos to counter the spread of Virus X on the planet SR-388. These creatures became a threat to the threat to the galaxy when Mother Brain, leader of the space pirates, seized control of them by assaulting Zebes. assaulting Zebes.

The mission was a success but, unfortunately, Samus was captured by the space pirates in their mothership when she tried to escape from the planet. Without a suit and armed only with her pistol, she not only manages to survive and escape from the mothership, but she also manages to find the Chozo God's Power Suit, which, compared to Old Bird's, was able to assimilate the old abilities of the which, compared to Old Bird's, was able to assimilate old Chozo abilities such as the plasma beam, the space jump and the gravity suit.

The Federation sends a group of soldiers to SR388. They return with information that the the metroids are swarming in the heart of the planet. There seems to be only one viable solution: send Samus to exterminate these monsters. There she discovers more advanced, more agile and more threatening subspecies. After defeating the queen who gave birth to the creatures, Samus discovers an egg. The egg hatches and a and a baby metroid emerges. Samus is ready to kill it, but the little creature shows no signs of hostility and so decides to spare her. As she prepares to board her ship, Ridley, out of nowhere out of nowhere, attacks her and gets her in trouble.