After Samus completed her mission and eradicated the entire Metroid population on SR388 as commanded by the Galactic Federation (sans the Metroid Hatchling, which she nicknamed "Baby"), she brought the Hatchling to the Ceres Space Colony for research. However, shortly after she left, she received a distress signal from the Station and returned to investigate.
When Samus arrives at the Space Science Academy where the Baby was being studied, she finds all the scientists slaughtered and the containment unit that held the Baby missing. Upon further exploration of the Station, she finds the Baby in a small capsule. As she approaches, Ridley appears and grabs the capsule. After a brief battle, Samus repels Ridley, and he activates a self-destruct sequence to destroy Ceres.
After escaping the explosion, Ridley flees to Zebes, and Samus goes after him.