Metroid Prime (Nintendo Cinematic Universe)

Metroid Prime is a Japanese anime film.

Summary
The space pirates make a clone of Samus called Dark Samus and its up to Samus to defeat the space pirates again and Dark Samus.

Plot Elements

 * Samus Aran intercepts a distress signal from the Space Pirate frigate Orpheon, whose crew have been slaughtered by the Pirates' own genetically modified, experimental subjects. At the ship's core, she battles with the Parasite Queen, a giant version of the tiny parasites aboard the ship.
 * The Parasite Queen is defeated and falls into the ship's reactor core, initiating the destruction of the ship.
 * While Samus is escaping from the frigate, she encounters a cybernetic version of Ridley called Meta Ridley. During her escape, an explosion damages Samus's suit, causing some of her abilities to malfunction.
 * Samus escapes the frigate and chases Ridley in her gunship towards the nearby planet Tallon IV.
 * After landing in the Tallon Overworld,
 * Samus explores nearby areas of Tallon IV and discovers the Chozo Ruins, the remains of the Chozo civilization. As she explores the ruins, she learns the Chozo on the planet had been killed by Phazon from a meteor that impacted on Tallon IV many years ago. After regaining her lost abilities in the ruins, Samus finds her way to the Magmoor Caverns, a series of magma-filled tunnels, which are used by the Space Pirates as a source of geothermal power.
 * Following the tunnels, Samus travels to the Phendrana Drifts, a cold, mountainous location which is home to an ancient Chozo ruin and Space Pirate research labs used to study the Metroids.
 * After obtaining new abilities, Samus explores the wreckage of the crashed Orpheon and then infiltrates the Phazon Mines, where she learns the outcome of the Phazon experimentation project, including the Metroid Prime, a creature that had come to Tallon IV with the meteor.
 * Advancing deeper into the mines, Samus fights her way through the Phazon-enhanced Space Pirates and obtains the Phazon Suit after defeating the monstrous Omega Pirate.
 * Samus discovers the Artifact Temple that the Chozo built to contain the Metroid Prime and to stop the Phazon from spreading over the planet.
 * To gain access to the meteor's Impact Crater, Samus collects and unites the twelve Chozo artifacts.
 * As Samus returns to the temple with the artifacts, Meta Ridley appears and attacks her.
 * Samus defeats Ridley and enters the Impact Crater, where she finds the Metroid Prime. After she defeats it, the Metroid Prime absorbs Samus's Phazon Suit and explodes.
 * Samus escapes the collapsing crater and leaves Tallon IV in her ship.
 * While looking for the Marines near Aether, Samus's ship is damaged by severe lightning storms from the planet.
 * Said storms have caused electromagnetic interference that prevented the Marines from communicating with the Federation.
 * Samus finds the troops dead and surrounded by hive creatures called Splinters.
 * The deceased Marines suddenly rise and attack her, apparently possessed, and she fights them off.
 * Samus then encounters her evil doppelgänger, Dark Samus, for the first time, and after a small skirmish Dark Samus jumps through a portal.
 * Samus decides to follow her through it and ends up on Dark Aether, a vile trans-dimensional duplicate of Aether, where she is attacked by a group of dark creatures called Ing, who capture Samus and after stealing the weapons from her suit throw her back through the portal.
 * Upon returning to Aether, Samus learns that the Marines were attacked and killed by Ing-possessed Splinters, and decides to enter a nearby alien temple structure to look for clues. When she reaches the structure, she meets U-Mos, the last remaining sentinel of the Luminoth, an alien race that have fought against the Ing for decades. They are now on the verge of defeat. He tells Samus that after a meteor struck Aether, the impact was so devastating, it created "Dark Aether", from which the Ing spawned. He also tells Samus that the Ing have taken virtually all of the 'Light of Aether', the entire collective planetary energy for Aether that keeps the planet stable, and begs her to retrieve it, for if either world gains all this energy, the other will perish.
 * Samus goes to three regions—the Agon Wastes, a parched, rocky, desert wasteland region; Torvus Bog, a drenched swamp area that houses a partially submerged hydrosubstation; and the Sanctuary Fortress, a highly advanced cliffside fortress built by the Luminoth filled with corrupted robots that serves as the Ing hive in Dark Aether—to retrieve the Light of Aether and return it to the Luminoth temples.
 * Samus fights Space Pirates, Dark Samus, and monstrous Ing guardians on her mission.
 * After Samus retrieves three pieces of the Light of Aether, she enters the Ing's Sky Temple and faces the Emperor Ing, the strongest Ing who guards the remaining Light of Aether.
 * Samus defeats the creature and retrieves the last remaining energy, causing Dark Aether to become critically unstable and collapse; however, her path out of the temple is blocked by a horribly altered and unstable Dark Samus.
 * After defeating her foe, Samus escapes as the dark world disappears around her.
 * Returning to U-Mos, Samus finds that the Luminoth were in a state of hibernation but have now awakened.
 * After a brief celebration, Samus leaves Aether in her repaired gunship.
 * Fleet Admiral Castor Dane, the commander of a Galactic Federation flagship Olympus, calls for a meeting with Samus Aran and three other bounty hunters—Rundas, Ghor, and Gandrayda.
 * The bounty hunters receive orders to clear a computer virus from several organic supercomputers called "Aurora Units", located throughout the galaxy.
 * The meeting ends abruptly when Space Pirates attack the Federation fleet.
 * Samus and the other bounty hunters are deployed to the planet Norion, where the Space Pirates are concentrating an attack on the Federation base.
 * While suppressing the attack, Samus learns that a Phazon meteoroid, called a Leviathan Seed, will soon collide into Norion.
 * Samus and the other bounty hunters attempt to activate the base's defense systems, when they are suddenly attacked by Dark Samus.
 * With the other bounty hunters knocked out, a severely wounded Samus manages to activate the system just in time to destroy the Leviathan Seed before she falls unconscious.
 * A month later, Samus awakens aboard Olympus, where she learns that Dark Samus's Phazon-based attacks have corrupted her.
 * The Federation equips her suit with a Phazon Enhancement Device (PED) that enables her to harness the Phazon energy within herself. She is informed that her fellow bounty hunters, also corrupted with Phazon and equipped with PEDs, have gone missing during their missions to investigate several planets embedded with Leviathan Seeds.
 * Samus is first sent to the planet Bryyo and later Elysia to determine what happened to her missing comrades. She soon discovers that both planets and their inhabitants are slowly being corrupted by the Leviathan Seeds and that she must destroy the seeds to reverse this.
 * Samus encounters heavy resistance from the Space Pirates, Phazon-corrupted monstrosities, and her fellow bounty hunters who have been corrupted by Dark Samus.
 * Throughout her mission, which eventually takes her to the Space Pirate homeworld, Samus slowly becomes further Phazon-corrupted. She manages to stop the Space Pirate assault with the assistance of the Federation troops.
 * After stealing a Leviathan battleship, Samus and the Federation fleet use it to create a wormhole that leads to the planet Phaaze, the origin point of Phazon.
 * Samus travels to the planet's core, where she finally defeats Dark Samus and then the corrupted Aurora Unit 313. As a result, Dark Samus is obliterated, and Phaaze explodes, rendering all Phazon in the galaxy inert.
 * The Federation fleet escapes Phaaze's destruction, but loses contact with Samus in the process. Samus eventually appears in her gunship, and reports that the mission is accomplished before flying off into space.
 * Samus returns to Elysia, where she mourns the loss of her fellow bounty hunters.
 * Post-Credits Scene: Samus is seen flying into hyperspace, with Sylux's spaceship following her.