Raid on Planet Zebes

The Raid on Planet Zebes was Samus Aran's final mission on Zebes, during Super Metroid. It was her second mission to Zebes, after her original Zero Mission.

Zero Mission
The Space Pirates had based their operations on Zebes before during Metroid: Zero Mission. Led by the corrupted Chozo supercomputer Mother Brain, the Pirates sought to clone Metroids stolen from the Galactic Federation using Beta-Rays. After Samus destroyed this operation, the remaining Pirates on Zebes began to rebuild their base, as well as Mother Brain, while other members of their race sought the mutagenic substance, Phazon, throughout the cosmos. This distracted the Federation and Samus from Zebes, allowing the Pirates to rebuild their base there undisturbed.

Ceres Space Colony
Following Phazon's eradication, Samus had been commissioned by the Federation to eradicate the Metroids on their homeworld, SR388. Samus spared the life of an infant that spawned in front of her and imprinted her. Calling it the baby, she brought it to the Space Science Academy on Ceres Space Colony in the hopes that the researchers there could study the Metroid. They discovered that the Metroids have the ability to give energy to bioforms, as opposed to siphoning it. Satisfied that research was well underway, Samus left the Colony.

Moments later, it was attacked by the Space Pirate leader, Ridley, who stole the baby and set the Main Computer of the colony to detonate. Samus pursued Ridley to Zebes, and set out to recover the baby at all costs. While she fought her way through the caverns of Zebes, the Space Pirates again used Beta-Rays to clone the baby. However, the excessive amount of Beta-Rays used on a single Metroid triggered an anomaly in its evolutionary cycle, causing it to become a Big Metroid rather than an Alpha Metroid.

The New Operation
Samus discovered that the Pirates were operating in nearly every sector of Zebes, and that the heart of their operation, Tourian, was again guarded by Golden Statues linked to the lifesigns of four Pirate leaders. To access Tourian, Samus would have to kill each leader.

She began with Kraid in Brinstar. Kraid, previously defeated during Samus's Zero Mission, was back and even stronger, but Samus was able to destroy him. Entering the Wrecked Ship, she eliminated the second of the four guardians, Phantoon, whose death allowed her to access the Gravity Suit, which would become necessary for the final two guardians. In Maridia, she murdered Draygon, the mother of the Evir creatures, before finally reaching the depths of Norfair for a confrontation with her nemesis, Ridley. She was able to defeat him once again, but in the next room found the baby's capsule broken and empty.

Tourian
Returning to the Golden Statues, Samus watched each one "die", before the entire sculpture sank into the ground and revealed the path to Tourian. Without wasting time, Samus entered Tourian and battled the Metroids cloned from the baby.

Samus entered a barren wasteland-like area in Tourian and found the dried husks of several creatures, having been killed by Metroid predation. She then encountered a massive Metroid and tried, but failed to escape it. It siphoned her energy until she had one unit left, before it recognized her as its "mother". The baby then fled, in shame. Samus restored her energy and continued on to the rebuilt Zebesian Command Center.

Final Conflict
Main article: Final Conflict

During the Final Conflict, Samus confronted a rebuilt Mother Brain, who attached herself to a mechanical body and unleashed a barrage of deadly attacks against Samus. She was eventually able to cripple Samus using the Laser Brain Attack. As she moved in for the kill, the baby entered and began to siphon her energy, before transferring it into Samus. Mother Brain somehow awoke, and killed the baby. Samus, fueled by the baby's energy and her own rage, unleashed the Hyper Beam against Mother Brain and finally destroyed her. Her death triggered a countdown sequence that would destroy the entire planet. Samus escaped with her life, but the universe lost the promise of the Metroids being used for good.

Aftermath
Samus, wounded from the battle against Mother Brain, returned to Galactic Federation Headquarters to publish her report. Ringleaders of a secret and illegal project salvaged fragments of the baby from Samus's Power Suit while she recuperated, and used them to clone Metroids on the BOTTLE SHIP. Samus fell into depression following the baby's death, feeling guilty over her failure to save it. Eventually, she would be led to the BOTTLE SHIP, and discover her role in the revival of the Metroids, merely weeks after she had eradicated them.