I typed up the full text from the Trilogy booklet.
(Would've gotten it up sooner but there weren't enough A.U. systems to back me up today. The rest of the processing power was partitioned for operating the new game release.)
Metroid Prime Trilogy History
No one knows when Phaaze was born.
A planet completely unique in an infinite universe, unlike any that came before it. Phaaze was alive. A conscious, sentient being.
Like all living creatures, Phaaze did its best to ensure the continued survival and prosperity of its race. Every 100 years, seeds, similar in form to meteors, would be fired from Phaaze to planets far away. These seeds, these children of Phaaze, were called Leviathans. Leviathans had the ability to generate wormholes, allowing them to travel to galaxies unbelievably far away.
When a Leviathan strikes a planet, it creates a Phazon Core which emits a strong toxin called Phazon all over the planet. Phazon is a powerful substance with the ability to completely corrupt living beings through genetic mutation. Over the course of a couple years, Phazon corrupts the entire planet, at which point the planet is reborn as a Phaaze clone.
Samus Aran, Bounty Hunter
Samus lived with here parents on the planet K-2L, a human colony in the Galactic Federation domain. When Samus was three years old, K-2L was attacked by a band of Space Pirates led by the brutal ruffian Ridley. When the Space Pirates left and the smoke cleared, a single figure remained standing. It was Samus Aran, the sole survivor of the attack on K-2L.
Samus was rescued from the charred ruins of K-2L by the Chozo, a race of beings who resemble giant birds. They had received the colony's distress signal during the attack, and came to assist. The Chozo took Samus back to their homeworld, Zebes.
Being a highly technologically advanced race, the Chozo crafted a power suit for Samus that gave her incredible strength. They trained her to become a fearsome warrior. Once her training was complete, Samus parted ways with the Chozo and became an intergalactic bounty hunter.
Samus carried out countless missions. Many that other bounty hunters deemed impossible. She became the most famed and capable bounty hunter in the universe, yet she was not fulfilled. Samus didn't become a bounty hunter to achieve fortune of fame. Her purpose was to avenge the death of her parents by slaying Ridley and the rest of the Space Pirates.
Before long, the opportunity to fulfill her purpose would arise.
The Battle Begins
Having established a reputation as an unstoppable warrior, Samus is summoned by the Galactic Federation, the sovereign government of a group of civilized planets.
Zebes, the planet where Samus was raised, has become the Space Pirates' base of operation. The Federation gives Samus orders to infiltrate the planet and eliminate the Space Pirates, along with the mysterious floating life-forms called Metroids. Metroids are reported to absorb energy from other creatures, and the Space Pirates are trying to use them as bioweapons. After battling her way through countless creatures and Space Pirates, Samus defeats Ridley, then demolishes Mother Brain, the central computer of Zebes' ecosystem and leader of the Space Pirates. Mother Brain's destruction causes the Space Pirates' base to explode. Samus narrowly escapes.
As fate would have it, some of the Space Pirates also escape the explosion on Zebes. A group of them leave in search of a power source to reinforce their soldiers with. They find Tallon IV, a planet struck by a Leviathan 50 years ago. The Space Pirates immediately begin using the mutagenic properties of Phazon to experiment on living things.
Three years after Samus's battle on Zebes, Samus is once again summoned by the Galactic Federation. After being briefed by the Federation, Samus travels to Tallon IV to investigate the reports of the Space Pirates. Nearing the planet, she intercepts a distress signal belonging to the Space Pirate ship Orpheon, which is in orbit around Tallon IV. Samus enters the ship and quickly discovers the cause of the distress signal: the Parasite Queen, a giant mutated creature born from the Space Pirates' Phazon experiments. Samus defeats the creature, but it falls into the ship's reactor, causing the ship to burst into flames. Samus loses almost all of the functions of her suit while escaping from the Orpheon. During her escape, Samus spots her nemesis, Ridley, genetically rebuilt following their fight on Zebes. Ridley flies off towards Tallon IV. Samus gets back to her ship and follows him to the planet's surface.
While Exploring Tallon IV, Samus discovers ruins from the Chozo civilization. Almost as if the Chozo knew she would find her way there, Samus discovers there is an item hidden on the planet that can restore the Power Suit's lost functions. She also learns from inscriptions in the ruins that the Chozo had hoped to completely eliminate Phazon and believed that one day a savior would come to do just that. She decides to destroy the source of the Phazon along with the last of Space Pirates. The task is not an easy one. The Phazon radiates from the Phazon Core, located at the bottom of the crate where the Leviathan landed. The only entrance to the crater has been sealed by the Chozo with a mystical lock that can only be opened by finding 12 artifacts that the Chozo have hidden on the planet. Samus scours the planet for the artifacts, dispatching many enemies before finallly obtaining all 12.
As Samus makes her way to the crater, she is confronted by Ridley, the last hope of the Space Pirates. Samus crushes Ridley by exploring a weakness in his chest and continues to the crater.
When she reaches the crater, Samus encounters Metroid Prime, a Metroid that has mutated into a terrible creature after absorbing a great amount of Phazon energy from the Phazon Core. Metroid Prime, serving as the Phazon Core's guardian, attacks Samus and a fierce battle ensues. However, during the fight, a powerful ability hidden within Samus emerges. Empowered by the will of the Chozo, Samus harnesses the power of Phazon to defeat Metroid Prime. In its final moments, Metroid Prime grows unstable and attaches itself to Samus's Phazon Suit, tearing it from Samus before exploding.
It seemed that the Phazon threat had been eliminated, but this was not the case. After Samus left Tallon IV, the few remaining cells of Metroid Prime began to secretly multiply using the gene information taken from Samus's suit.
At about the same time the Leviathan landed on Tallon IV, another Leviathan arrived at a different planet.
The name of that planet was Aether.
Aether, where a race called the Luminoth had settled, was facing unprecedented danger due to the crash of the Leviathan. The impact from the Leviathan divided Aether into two dimensions: Dark Aether and Light Aether.
Dark Aether, a world where dark energy swirled freely, was home to a brutal, ruthless race called the Ing. Light Aether, on the other hand, was an enlightened world where the Luminoth lived in peace. Eventually, the Ing began to cross into the other dimension and attack Light Aether.
Samus is sent to Aether to investigate the disappearance of a squad of Galactic Federation soldiers. The soldiers had been in pursuit of Space Pirates in the area before communication with them was lost. Upon arriving at Aether, Samus is attacked by the Ing, and most of her suit's abilities are stolen. Samus then continues her exploration and finds that the missing Galactic Federation soldiers have been killed by the Ing. Investigating further, Samus meets U-mos, the chief of the Luminoth, and learns just how dire the Luminoth's situation is. U-mos knows that Samus is the Luminoth's only hope for survival, so he asks for Samus's help. She agrees to eradicate the Ing and destroy Dark Aether. If all of the planetary energy is restored to Light Aether, Dark Aether will cease to exist. Samus finds an Energy Transfer Module which transfers energy from Dark Aether to Light Aether.
Samus travels to dark Aether to combat the Ing horde. While battling the Ing, Samus is confronted by Dark Samus, her mirrored form that emerged from the remains of Metroid Prime on Talonn IV. Dark Samus has come to Aether to absorb Phazon in order to increase her power. Samus, able to travel between the light and dark worlds with the technology of the Luminoth, repeatedly does battle with Dark Samus, the Ing, and the Space Pirates, who are harvesting Aether's Phazon to use as a power source. Over the course of many battles with the Ing, much of the planet's energy is restored to Light Aether. At long last, she arrives at Dark Aether's headquarters, the Sky Temple.
Samus enters the Sky Temple and does battle with the leader of the Ing, Emperor Ing. After a fierce battle, she defeats Emperor Ing, withdrawing the last of Dark Aether's energy, which destroys Dark Aether. As Samus attmpts to escape the crumbling dimension, she is once again confronted by Dark Samus, whose form is now complete after absorbing a large amount of Phazon. Samus has interfered with Dark Samus' search for Phazon many times, and Dark Samus now views her as a mortal enemy.
Samus and Dark Samus engage in an epic battle while Dark Aether crumbles. Although Samus is at a disadvantage to the immense, Phazon-fuled power of Dark Samus, she hatches a plan to defeat her rival. Samus uses Dark Samus's own Phazon energy against her and destroys her darkened counterpart. Once the battle is finished, Samus returns to Light Aether, barely escaping disaster. The revived Lumintoh see her off, and Samus leaves Aether.
Will peace come once more to the galaxy?
Unbeknownst to our heroine, particles of Dark Samus's Phazon energy floated into space and began to mold themselves into human form.
Although peace returned to Aether, the Space Pirates continued to harvest Phazon from the planet. Little did they know, particles of Dark Samus that had floated into the space around Aether took notice of this activity. Once the pirates finished loading some of the remaining Phazon onto their ship, Dark Samus infiltrated the ship and made her way to the Phazon storage bay. There, she quickly absorbed all of the stored Phazon, allowing her to be reborn. And in the blink of an eye, the Space Pirates' ship and all aboard were brought under her control. They became puppets to her will. Anyone infected by Dark Samus's Phazon energy would obey.
While searching for Phazon energy to increase her power further, Dark Samus detects the faraway planet Phaaze, the original source of all Phazon. Dark Samus begins her trek across the galaxy to Phaaze. On the way, she encounters a Leviathan that appears from a wormhole. Dark Samus infects this Leviathan and is able to control it, giving her the power to open wormholes at will. This allows her to travel to Phaaze quickly. for Dark Samus, a chance to control the source of all Phazon is a chance to conquer the entire universe.
Upon reaching Phaaze, Dark Samus absorbs an enormous amount of Phazon, reaching an extremely high power level. With this new found power, she vows revenge against Samus and the Galactic Federation.
Dark Samus plans to gain control of the Aurora Units, the organic supercomputers that are the hub of the Galactic Federation network. They are loaded at important Federation bases and on important battleships. All Aurora Units are connected with each other in the broad network, making it possible to access an enormous database.
She attacks the Federation battleship Valhalla and grabs the Aurora Unit. She then installs the stolen Aurora Unit on Phaaze, causing it to be infected by Phazon. The infected Aurora unit allows Dark Samus to control Phaaze, giving her the ability to choose when and where to launch Leviathans.
First, Dark Samus sends a Leviathan to one of the Space Pirate homeworlds and places all Space Pirates completely under her control through the Phazon infection. Meanwhile, the Aurora Unit infected with Phazon sends the Phazon virus to the other Aurora Units in the Galactic Federation. Noticing that the Aurora Units seem to be infected by some kind of virus, the Galactic Federation disconnects them from the network and begins working on a vaccine. Being unable to use the network makes this process more difficult.
If the Federation came under attack at this point in time, they would be at a severe disadvantage. Therefore, they establish a base of operations in the battleship Olympus, a Federation ship orbiting the planet Norion. In order to deliver the vaccine to the Aurora Units and investigate the cause of the virus, the Federation summons four highly skilled bounty hunters: Samus, Ghor, Rundas, and Gandrayda.
Admiral Dane, the commander of the Olympus, and the four bounty hunters meet aboard his ship. During their strategy meeting, a group of Space Pirates led by Dark Samus suddenly attacks Norion.
At the same time, a Leviathan appears from a wormhole and charges toward the planet. The only way to stop the Leviathan is to reboot Norion's defense system, which has been knocked offline by Space Pirates.
With the help of Galactic Federation sold[i]ers equipped with PED suits, a new weapon that converts Phazon energy into offensive power, Samus and the other bounty hunters are able to stop the Space Pirates and destroy the Leviathan. However, just before they can reactivate Norion's defense system, Samus and the other bounty hunters are attacked by Dark Samus, who suddenly appears in the control tower of the defense system. The bounty hunters are knocked unconscious, and Dark Samus's Phazon energy is planted in their bodies.
A week passes before Samus regains consciousness in MedLab Delta on the Olympus. The Phazon infection inside the bodies of Samus and the other bounty hunters is confirmed, but luckily, there are no ill effects, and they are miraculously able to coexist. This means that the PED suits can harness the wearer's internal Phazon for increased power. The Galactic Federation gives Samus and the other hunters PED suits so they can utilize the Phazon in their bodies.
The Federation immediately asks Samus to eliminate the Phazon Cores that Leviathans have formed on the planets Bryyo and Elysia. She is also asked to administer the virus vaccine to the Aurora Units installed on Sky Town, a floating city created by the Chozo, located on the planet Elysia. Although the other three bounty hunters had already embarked on this same mission, none had been heard from since leaving, and they were presumed missing. The Federation also asks Samus to investigate their whereabouts.
Samus heads to Bryyo and enters Hyper Mode, a state of increased power fueled by Phazon energy. Hyper Mode makes Samus immensely powerful, but she notices that if she stays in Hyper Mode too long, something unusual happens. Whenever she activates Hyper Mode, the cells in her body that have been corrupted by Dark Samus's Phazon energy are activated. If Samus becomes overloaded with Phazon energy, the corrupted cells will take over her body and mind, placing her under Dark Samus's control.
Samus learns that the three other bounty hunters have already lost their will to Dark Samus, and are completely under her control. She reluctantly defeats the corrupted bounty hunters Rundas and Ghor, destroys the Phazon Core on Bryyo and Elysia, and administers the vaccine to Sky Town's Aurora Unit, which cures it.
The Galactic Federation receives a communication capsule that Gandrayda sent prior to becoming completely corrupted. From this capsule, the Galactic Federation learns the coordinates of the Space Pirate homeworld, and also learns that a Leviathan has landed there. Admiral Dane gathers a fleet of battleships and relays to Samus that they're heading to the Space Pirate homeworld.
Samus ventures on to the Space Pirate homeworld. The Phazon contamination in her body is progressing as time passes, and she doesn't have much more time before she is completely corrupted. Samus encounters Gandrayda, the last corrupted bounty hunter, and destroys her. The Galactic Federation fleet arrives, and Samus asks them to lower the defense shield that protects the Space Pirate base. Samus makes her way to Phazon Core with the help of Federation solders. When she reaches the core, she is assaulted by her nemesis, Ridley, who has been rebuilt again and strengthened since their last fight. After a vicious fight, Samus dispatches Ridley and destroys the Phazon Core.
Finally, after myriad battles, the time comes to assault Phaaze, Dark Samus's headquarters and the source of all Phazon.
Samus and the Federation fleet travel to Phaaze after Samus opens a wormhole by controlling a Leviathan. The Space Pirate army is guarding Phaaze, and a fierce battle breaks out between the Federation fleet and the Space Pirates. During the battle, Samus lands on Phaaze by herself. The high concentration of Phazon on Phaaze is almost too much for Samus to handle, and it's only a matter of time before she is completely corrupted. Dark Samus, now at her most powerful, appears before Samus as she heads to the core of Phaaze, and the two superpowers engage in battle. Dark Samus joins with the stolen Aurora Unit, raising her power to unheard of levels. The battle rages on with an intensity unequalled in all space and time. Harnessing the power of Phazon with her PED suit, Samus finally destroys Dark Samus and the infected Aurora Unit, which also destroys the Phazon in Samus's body.
When Dark Samus is destroyed, Phaaze begins to collapse, and Samus races to escape the planet. Admiral Dane orders the Federation fleet to retreat through the open wormhole, which disapears just as the last ship in the fleet flies through in it.
And with that, the battle is over. However, Samus is nowhere to be found. Just when they've given up hope of Samus's survival, a communication from Samus appears on the command screen of the Olympus:
Samus's ship flies off into the depths of space, thus closing the curtain on the story of Phazon.