Metroid Prime, despite the name, is actually not any species of Metroid. Its designation was given to it by Space Pirate scientists who noted the similarities between the way the alien drew strength and power from Phazon and the way Metroids did so from the energy of living things. Metroid Prime's limitless hunger for Phazon causes it to continuously mutate, growing in size and power. Its insatiable appetite continued even after its defeat at the hands of Samus Aran, ripping away her Phazon Suit enhancement and being reborn as the Phazon entity known as Dark Samus.
The Chozo lore entries in Metroid Prime tell of a prophecy that foretold a 'Worm' that would consume the planet of Tallon IV, bringing with it a 'Great Poison'. It also foretold 'The Entrusted One' who would confront the Worm and deliver the planet from evil. The Worm was Metroid Prime, at the heart of a Phazon meteor called a Leviathan, that crashed onto Tallon IV about 50 years prior to the events of Metroid Prime. It dug itself into the core of the planet and began to spread its 'Great Poison', Phazon. The Chozo who came into contact with the Phazon became mad, turning into 'Turned' that would attack their fellow Chozo and destroy anything they came across. Even after their death, the 'Turned' remained on Tallon IV as dangerous Chozo Ghosts.
As the corruption spread, the desperate Chozo built a temple around the Leviathan to contain it and the corruption it was spreading. They named the temple the 'Cradle', and sealed it with twelve artifact keys, scattering them across the planet. It was too late to save the planet, however, and eventually the corruption spread all over the planet. Eventually, the Chozo died out or left Tallon IV, leaving only their insane ghosts and the few relics that remained intact.
Years later, the Space Pirates would come to Tallon IV and discover Phazon, the artifact temple, and Metroid Prime. They would be followed by 'The Entrusted One', Samus Aran, who would disrupt their operations and eventually enter the Worm and face its guardian, the Metroid Prime.
Metroid Prime has two forms. The first has spider-like chitinous armor, completely impervious to all attacks, except for its weak point, the eyes. Metroid Prime's armor also has a power-shift property, its current color depicting what beam weapon it is currently vulnerable to: yellow is Power Beam, purple is Wave Beam, white is Ice Beam and red is Plasma Beam. Only attacks made from the corresponding weapon or charge combo can harm Metroid Prime.
Its color also affects the property of its attacks: the beam of energy it shoots from the mouth in its underbelly and the slow-moving energy orbs that it launches. These attacks can freeze Samus if Metroid Prime is white, disrupt her visors when purple, and burn her when red. Prime also has cluster missile launchers, a tractor beam, and a deadly charge attack which can only be avoided by activating Morph Ball and entering one of the grooves in the floor. Once Samus defeats the armored form, Prime retreats deeper into the Leviathan with Samus in pursuit. At the very heart of the Leviathan, she finds Metroid Prime has cast off its armor, revealing its core essence.
Metroid Prime's core will lash at Samus with its tentacles and create groundquakes which can only be evaded with the space jump. As well as these direct attacks, Metroid Prime will create pools of Phazon which will spawn standard, Hunter, and finally Fission Metroids as the fight progresses. After spawning Metroids, Prime will turn invisible. Samus can only track Prime with the X-Ray Visor at this point. Once located, the beast can be damaged when Samus stands in the pool of Phazon. Standing in the pure Phazon Samus activates Hypermode, allowing Samus to fire a stream of pure Phazon. Firing the beam uses up the Phazon in the pool. Samus must wait for Prime to generate more once the first pool is gone.
After creating the next Phazon pool, Prime will yet again change its visible spectrum, this time only traceable with the Thermal Visor. This cycle repeats (Combat Visor, X-Ray Visor, Thermal Visor) until Samus does enough damage to Metroid Prime. At this point, the boss destabilizes. In a last-ditch effort, it latches onto Samus, pulling the Phazon Suit upgrade from her. Samus flees as Metroid Prime and the Phazon inside the Leviathan becomes unstable, escaping to her gunship in time to see the artifact temple collapse from the resulting explosion.
In the secret ending to Metroid Prime, players are shown the inside of the Leviathan after its collapse. Laying in the cavern is a single pool of Phazon, which ripples and shakes as a conspicuous arm juts from the substance, wearing Samus's Phazon Suit. Metroid Prime had absorbed her suit and part of her DNA, allowing it to be reborn as Dark Samus.