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Metroid Prime – The Full Trilogy Story Explained

With the physical launch of Metroid Prime Remastered on the horizon, fans are eager to dive back into the world of Metroid and relive some childhood experiences. However, the story doesn’t just stop at the first game as the Metroid Prime trilogy features a densely layered and captivating sci-fi narrative very different from what we’ve seen in the previous Metroid games. We’ve decided to explore the full story of the Metroid Prime Trilogy, going through each game in the series.

Before we begin, it’s worth noting that the Metroid Prime games offer a very different gameplay perspective. Instead of the side-scrolling of the mainline games, Metroid Prime features a first-person perspective with combat occasionally broken up by third-person segments for traversal. The story of the Metroid Prime Trilogy is also set between the events of the first Metroid and Metroid II: Return of Samus.

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Metroid Prime

Metroid Prime Full Trilogy Story Explained

Galactic bounty hunter Samus Aran intercepts a distress signal from the Space Pirate frigate Orpheon. Upon boarding the ship, Samus learns that the crew were slaughtered by their own genetically modified, parasitical subjects. Samus encounters The Parasite Queen at the core of the ship. She defeats the creature but its corpse falls onto the ship’s reactor core, causing Orpheon to destruct and plummet to the nearby planet Tallon IV. During her escape, Samus encounters a cybernetic version of Ridley (the main antagonist of the Metroid series) called Meta Ridley.

After landing on Tallon IV, Samus discovers the Chozo Ruins, the remains of a civilisation called the Chozo. Several decades ago, a meteor impacted the planet and released a plague called “The Great Poison” (or Phazon as called by the Space Pirates) which wiped out the Chozo race. Samus explores the planet’s various regions before discovering Space Pirates research labs that were studying the Metroids.

Samus explores the wreckage of the Orpheon and then the Phazon Mines, where she learns that a creature called the Metroid Prime had arrived on Tallon IV with the meteor. Samus defeats several Phazon-enhanced Space Pirates and obtains the Phazon Suit. She stumbles upon the Artifact Temple that the Chozo constructed to contain the Metroid Prime and sets out on a journey to collect twelve Chozo artifacts that give her access to the meteor’s Impact Crater.

Samus runs into Meta Ridley and defeats it while returning to the temple. She enters the ruins only to discover the Metroid Prime alive and contained. Samus battles the creature but not before it absorbs her Phazon Suit, causing it to explode. Samus escapes the temple’s collapse and leaves Tallon IV on her ship. If players collect every item in the game, a bonus cutscene plays out that shows the Metroid Prime reconstructing itself into a body resembling Samus.

Metroid Prime 2: Echoes

Metroid Prime Full Trilogy Story Explained

Some time after the events of the first game, Samus is searching for Galactic Federation Marines on a planet called Aether. Her ship is damaged by a lightning storm, which also cuts communication with the Marines. Samus finds the Marines dead and surrounded by creatures called Splinters. The dead Marines, seemingly possessed, rise to attack her but she fends them off. Samus is suddenly confronted by her doppelganger, Dark Samus, who she chases through a portal that transports her to Dark Aether. She is attacked by creatures called Ing and flung out of the portal after all her weapons are taken.

Samus learns that the Marines were killed by Ing-possessed Splinters. She journeys to a nearby alien structure to look for clues, but comes across U-Mos, the last remaining sentinel of an alien race called Luminoth. U-Mos explains that his race fought the Ing for decades and are now on the verge of defeat. Long ago, a meteor struck Aether but the force was so powerful that it created Dark Aether and spawned the Ing.

U-Mos tells Samus that the Ing have taken the ‘Light of Aether’, the entire collective planetary energy that keeps Aether stable. He asks Samus to retrieve it. To reclaim parts of Aether’s energy, Samus uses an energy transfer module. Throughout the game, she journeys to various dangerous regions to reclaim the Light of Aether and return it to the Luminoth temples, while also running into Dark Samus and Space Pirates.

Once Samus collects three pieces, she enters the Ing’s Sky Temple and defeats Emperor Ing who guards the last Light of Aether. This causes Dark Aether to become critically unstable and collapse. On her way out, Samus encounters Dark Samus once again, this time terribly transformed. She defeats her foe and exits the portal as Dark Aether and the Ing disappear forever. The Luminoth are awakened from their hibernation and Samus leaves in her repaired ship. A bonus ending shows Dark Samus reforming herself above Aether.

Metroid Prime 3: Corruption

Metroid Prime Full Trilogy Story Explained

Set six months after the events of Echoes, Metroid Prime 3: Corruption begins with Samus being called for a meeting aboard the Galactic Federation’s flagship GFS Olympus. Samus, along with three other bounty hunters named Rundas, Ghor and Gandrayda, are tasked with clearing a virus from organic supercomputers called Aurora Units, located throughout the galaxy. The meeting is cut short when Space Pirates suddenly attack the Federation Fleet. Samus and the bounty hunters are deployed to the planet Norion to defend the main Federation base.

Samus learns that a Phazon meteor called the Leviathan Seed will soon collide with Norion. Together with the other bounty hunters, she attempts to activate the base’s defence systems but is interrupted by Dark Samus who knocks her unconscious, but not before she’s able to activate the system just in time to destroy the Leviathan Seed and save Norion.

A month later, Samus wakes up aboard Olympus, learning that Dark Samus’s Phazon attacks corrupted her. The Federation upgrades her suit with the Phazon Enhancement Device (PED) that allows her to use the Phazon energy within herself. After learning that her fellow bounty hunters were also corrupted by Dark Samus, she travels to various planets to uncover what happened to them. Samus learns that both planets Bryyo and Elysia are being corrupted by the Leviathan seeds and must destroy the seeds to reverse this, meeting retaliation from the corrupted bounty hunters along the way.

Samus goes to the home planet of the Space Pirates and stops an assault with Federation troops but she’s slowly growing more corrupt due to Phazon. She steals a Leviathan battleship and then uses it to open a wormhole to the origin planet of Phazon, called Phaaze. Here she fights Dark Samus for the final time as well as the corrupted Aurora Unit 313, destroying Phaaze in the process and rendering all Phazon in the galaxy inert. Samus returns to Elysia and mourns the death of the bounty hunters before flying into hyperspace – pursued by a certain spaceship…

Metroid Prime Remastered receives a physical release on 3 March 2023 exclusively for Nintendo Switch.