Samus charged up the stairways, and raised her armcannon as she saw a group of warriors clothed in green phazite armor appear, wielding halberds in their grasps. One pointed forward at her, and yelled out "Kill the heretic. Kill it!" Two of them raised their gauntlets, and orbs of phazon burst from them. Samus sidestepped the attack, and fired off several shots. The nearest warrior took the blunt of the attack, and collapsed forward, rolling down the rest of the stairs. Samus leaped over the carcass and fired a missile, only to see it deflected aside by a halberd strike.

As her momentum decreased, one of the guards fired a barrage of bolts from his gauntlet, but missed as Samus transformed into a morph ball form, who then boosted forward, slamming the guard backwards into the stairs, cracking them. Morphing back, she fired several more blasts, causing another guard to collapse. She then quickly lowered herself as a halberd swung overhead, narrowly avoiding being beheaded. Spinning about, her foot smashed into the guards face, a loud crack emanating as he was sent flying backwards down the steps, leaving only one guard standing.

The head guard swung his halberd, causing Samus to sidestep it, but as she did, the guard fired a bolt of phazon from his gauntlet, striking Samus in the shoulder. The attack burning her flesh even through her armor, causing her to grimace in pain from behind her mask. Raising her cannon, she fired a missile that burst forward, smashing into the guard’s chest. As the smoke cleared, the guard could be seen dazed, his chest bleeding, when Samus raised her other arm, a beam of energy bursting from it and wrapping around its leg. Swinging her arm aside, the grapple beam flung the guard aside, sending him flying off the edge of the stairs.

With the small fry out of the way, Samus entered the temple, wary of any more guards. As she passed the artifacts around her, she noticed that no guards were in sight. Her gaze then fell upon the giant statue of a familiar old foe before her. As she approached it, she stopped as a rumbling noise emanated from behind the statue, which began to rock back and forth.

The statue exploded, sending shards flying in all directions. Covering her eyes, she slowly looked on, seeing a blue cloud of phazon flowing out a newly revealed tunnel. Raising her arm cannon, she saw an elongated arm stretch out of the haze, its sharpened claws gripping the sides of the tunnel, followed by a second one made entirely out of orange phazite. She watched on as the rest of the body was dragged out, and after several moments she realized it was the High Prophet. Its fur was gone, replaced by blue, phazon enhanced muscle structures, its eyes enlarged and bleeding pure phazon, its jaws elongated as its tongue, nearly twice its original length, hung limply out of it, and finally an array of phazite spikes protruded from its back.

With a roar the monstrosity leaped forward at Samus, its eyes filled with malice. Samus quickly responded by leaping over it, fired several plasma bolts into its exposed back. The beast roared, whether in pain or in anger Samus did not know. As she landed onto the ground, she was suddenly sent flying sideways by a swing of the beasts tail. As she crashed through several statuettes, she spun about, firing a super missile at the now open maw of the prophet.

The head of the High Prophet was instantly engulfed in flames for a moment, and as the smoke cleared, its bloodied mouth was visible, several of its teeth falling to the ground. It suddenly roared, and then charged forward in leaps and bounds, raising its phazite claw as it did so. As it tore through the wall with ease, the claw then came down sharply, nearly cutting through Samus had she not rolled out of the way. Focusing on the Morph Ball, the beast opened its jaws, and then fired a massive beam of phazon energy.

Samus was sent flying through the air, and upon hitting the ground, returned to her normal form. As the beast slowly began to walk towards her, Samus fired off a missile. The High Prophet easily dodged it, but then slowly turned about as a cracking noise was heard. Looking behind it, it saw a pillar slowly crumble at the spot where the missile had struck, and within seconds the entire structure fell forward onto the mutant. With a mighty crack the pillar slammed down upon its biological arm, shattering the bones within it instantly.

Pinned beneath the pillar, the High Prophet let out a roar in agony. As Samus rose from the ground, she charged her ice beam and took aim. The mutant suddenly began to glare, and then raised its free arm, the one made of phazite, and brought it down sharply... severing off its broken, trapped arm. As torrents of blood and phazon flowed from the open wound, the High Prophet bounded forward, overcome with rage, and prepared to take down Samus.

Still holding still, she watched on as the beast continued to charge her, and then, just as it leaped skyward in order to pounce upon her, she opened fired. The effects were nearly instant as the Ice Spreader struck her foe, its icy grasp slowly engulfing it in ice. Its momentum still moving it forward, Samus was forced to leap aside in order to avoid a collision.

As the High Prophet slammed into the ground, part of him shattered on impact, obliterating his other arm and the lower half of his body. Gasping in pain as his life slowly left his body, he suddenly spoke, surprising Samus, and said "My... master... will... avenge... me..." and with that, a gush of phazon escaped his jaws as a gurgling sound was heard from within his throat, after which his head went limp.

Looking on, Samus saw the body begin to deteriorate, particle of phazon escaping it until the entire body had vanished. The cloud of phazon hovered in midair for a moment, and then burst towards the open tunnel, vanishing into the darkness. Watching on, a brilliant blue glow began to fill it, and then out of the darkness floated Metroid Prime.

Samus instantly raised her arm cannon and repeatedly fired her Power Beam at its main body. Appearing to be unharmed, Metroid Prime telepathically roared "You stand no chance... You were weakened just by that worm, and he simple fed off my power.... I will annihilate you." Energy began to build up in its tentacles, and was then released all at once, sending a massive shock wave of phazon at Samus, sending her flying backwards, smashing through a pillar before she was sent soaring out the temples entrance and skidding down the rest of the stairs.

Slamming into the courtyard, Samus attempted to painfully get up, just in time to see Dark Samus aiming her arm cannon at her, the guards who had been outside before now only a distant memory, their phazon-infused ashes blowing into the wind along the crater filled ground. Dark Samus let out a hollow laugh, the massive amount of phazon she had absorbed still affecting her, when she stopped and looked up just as the temple exploded in a cloud of phazon. Metroid Prime could be seen floating in the center of ruins, his gaze meeting Dark Samus'.

Raising her arm cannon away from Samus' head and towards the self-proclaimed deity, her intentions were made clear....

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