SR-388 incident

“	Samus Aran... You must exterminate the Metroids once and for all!	„
—Supreme Council

Samus stands atop her Gunship after landing on SR388 in Metroid: Samus Returns.

The SR-388 incident was a mission carried out by Samus Aran on the planet SR388, to eradicate the Metroid species once and for all. It is chronicled in Metroid II: Return of Samus and Metroid: Samus Returns.

Background

Chozo

The Chozo seal away the Metroids.

At some point many years prior to the birth of Samus, the Thoha tribe of the Chozo landed on a desolate planet named SR388, and proceeded to build a colony. They discovered that the planet's soil and creatures were rich with an abundant energy source, Aeion, and built mining robots to harvest it. At the same time, they discovered a gelatinous, parasitic yellow life-form that could infect creatures and kill them, before assuming their forms and turning them into horrible beasts. Knowing the threat this parasite (named X) posed to the cosmos if left unchecked, the Chozo created the Metroids to prey upon them, greatly reducing their numbers. The Metroids were engineered to be invulnerable, save for exposure to extremely cold temperatures, and to quickly drain an X Parasite of its life energy. They were able to harvest this energy for scientific possibilities, turning SR388 into a thriving colony.

Unexpectedly, the Metroids began to evolve into larger, and deadlier forms (it is implied in the unlockable Chozo Memories that this was because of a reaction to Aeion), and multiplied to the point of being uncontrollable. Once again, the Chozo were forced into survival mode and sought to contain the Metroids as they, too, had become a threat to the galaxy. Unable to destroy the Metroids, the Chozo decided to seal them away, and prevent any nefarious parties from using them for their own gain. The Chozo separated groups of Metroids into each area using a purple liquid that would put the native wildlife, including the Metroids, into stasis, while being toxic to offworld entities. They implemented Chozo Seals to control the levels of liquid, which could only be unlocked by killing all of the Metroids in a given area, collecting strands of their DNA, and uploading it into the seal. Deeming the planet a lost cause, the Thoha Chozo planned to destroy SR388, but were betrayed by the Mawkin tribe's leader Raven Beak who sought to use the Metroids in his bid for galactic conquest. After executing all the Thoha save for Quiet Robe, the Mawkin Chozo retreated from SR388 and planned to return to collect Metroid samples on a later date.

The Chozo security system was only partially effective. While it kept most of the Metroids in stasis for many years, some Metroid larvae were able to escape to the Surface, and were captured by Galactic Federation researchers aboard the Space Research Vessel Marina. The researchers came to the same conclusion as the Chozo: that while the Metroids had enormous scientific potential, they could also be extremely dangerous in evil hands. Unaware of their natural life cycle, the researchers also discovered that a Metroid larva could easily be multiplied by exposing it to Beta-Rays.

Samus Aran and the Metroids

Samus lands on SR388 (Metroid II).

On its way back to Galactic Federation Headquarters, the Marina was attacked by a group of Space Pirates seeking to steal the Metroids. The Pirates were able to capture a specimen, and took it to their stronghold on planet Zebes, where they began to clone the Metroid in order to overtake the galaxy. The Federation attempted to attack Zebes, but failed. Out of desperation, they hired the enigmatic Bounty Hunter Samus Aran to infiltrate Zebes alone, to exterminate the Pirates' Metroid specimens, and defeat their leader, the rogue supercomputer Mother Brain. Samus completed her mission, while also defeating her arch-nemesis Ridley, and destroying the Space Pirate Mother Ship on the planet's surface.

Now a legendary savior of the galaxy, Samus continued to fight the Space Pirates' schemes to use Metroids over the course of many years. Her battles with the Pirates and Metroids, as well as the mutagenic substance Phazon, led to the Space Pirate forces becoming severely weakened and Ridley being defeated once again. At some point following these battles, the Galactic Federation came to the decision that the Metroids must be exterminated. They sent a research team to investigate SR388, but soon lost contact with the team. The Galactic Federation Special Squadron that was subsequently sent also went missing soon after landing. Given her experience with the Metroids, Samus was tasked by the Federation to finish the teams' missions and eradicate the Metroids once and for all.

The Mission

Arriving on SR388, Samus began her mission, proceeding deep into the underground caverns. She discovered Aeion Ability Artifacts that were compatible with her Chozo Power Suit, which enhanced her skills and abilities. She also discovered the Metroid life cycle, with each form evolving to become stronger than the last. Samus hunted the Metroids one by one, collecting their DNA after each kill and channeling it into the ornamental Chozo Seals, which removed the lakes of purple liquid and allowed her to move deeper into SR388, to the stronger Metroids. During her journey, she also encountered the Diggernaut, a massive Chozo mining robot that perceived her as a threat and chased her through an extensive mining cavern. After escaping, Samus came across it again in Area 6 and destroyed it.

The baby imprints onto Samus.

Her conquest through SR388 eventually led her to the Metroid hive, where she encountered newly hatched Metroid larvae before finally confronting the massive Queen Metroid in its nest. After a grueling battle, Samus defeated the Queen, who fell dead before her. Believing her mission complete, Samus continued on past the Queen, but soon came across a Metroid Egg. As she examined the egg, it hatched and produced an Infant Metroid. Samus quickly readied to shoot it with her Ice Beam. To her surprise, the creature was docile, and hovered around her as a confused child. Unable to bring herself to destroy the baby, Samus lowered her weapon and proceeded to leave. The baby carved out walls of otherwise indestructible crystals for its adoptive "mother" as they continued to her Gunship.

Returning to the Surface, Samus discovered that the sky had darkened considerably and a massive storm was brewing. As she approached her Gunship, Proteus Ridley appeared from the skies and snatched up the baby. Ridley had recovered from his previous defeat and made haste to SR388 to recover the Metroids before Samus destroyed them. Samus immediately sprung into action and engaged Ridley in a deadly battle over her "child". At one point, Ridley overwhelmed her and prepared to finish his nemesis off when the baby charged in and drained Ridley of some of his energy (transferring it to Samus), allowing her to get out from under him and continue the fight. With assistance from the baby, Samus attacked Ridley until his remaining cybernetics short-circuited and he fell to the ground, defeated. Afterwards, Samus then left SR388 with the baby.

By the time Raven Beak was ready to return to SR388, Samus had already completed the extermination mission, further delaying his plans.

Aftermath

Mother Brain kills the baby.

Samus's decision to spare the baby had long-term repercussions that are seen in the subsequent Super Metroid, Metroid: Other M, Metroid Fusion and Metroid Dread.

Having seen the life-saving ability that the baby demonstrated during the battle with Proteus Ridley, Samus believed it had enormous potential to benefit galactic civilization, and took it to the Space Science Academy on Ceres Space Colony for study. Some time after the battle, Ridley recovered and left SR388 in pursuit of Samus. He ravaged Ceres and made off with the baby to the rebuilt base on Zebes. Samus followed him there, and ultimately destroyed him, the Space Pirates, the newly cloned Metroids, Mother Brain, and the entire planet itself.

During the battle against Mother Brain, she killed the baby over Samus's head, and particles from it adhered to her Power Suit. These fragments would be extracted from her suit during her recovery aboard the Galactic Federation mothership, where the ringleaders resurrect the Metroids aboard the BOTTLE SHIP's Sector Zero and are genetically engineered to be unfreezable. The revived Metroids are destroyed by Adam Malkovich's sacrifice.

Meanwhile, with the Metroids extinct, the X Parasites are able to make their resurgence on SR388. Samus finds herself back on the planet to aid the Biologic's research team as they conduct a survey, but is infected by the X and nearly killed. She is administered a vaccine created from fragments of the baby Metroid, saving her life and rendering her immune to the X. Soon after, an X outbreak occurs on the Biologic Space Laboratories research station, where Samus once again discovers that the Galactic Federation have attempted to resurrect Metroids, but the Restricted Laboratory housing them are soon destroyed by the X. Realizing the danger that the X posed, Samus set the station on a collision course with SR388, exterminating the parasitic race.

With Samus having acquired Metroid DNA from the vaccine, she became a target for Raven Beak. He anonymously sent footage to the Galactic Federation and Samus of a live X on ZDR, luring the E.M.M.I. and Samus. After capturing and reprogramming the E.M.M.I. to seize Samus's DNA, Raven Beak confronted and defeated Samus on her arrival, triggering the awakening of her Metroid powers. He then left her in a stress-induced environment, including releasing quarantined X Parasites from Elun, so that she could fully awaken these powers, then planned to create and clone an army of Samus herself once she became the most powerful Metroid in existence. Unfortunately for Raven Beak, an enraged Samus activates the full potential of her Metroid powers, ultimately destroying him, the X threat, and the planet.