The Omega pirate ran through the jungle, toppling any tree that got in its path. It grabbed the stump where its hand used to be, and let out another painful moan. After several moments, it refocused on its mission to find the phazon source that was located up ahead. The squads, the Elite Commando Unit Omicron, had been sent ahead before it should have completed their objectives hours beforehand, but for some unknown reason or another they failed to return to the extraction point or even answer their transmissions.
The Omega then recalled the Hunter it had fought earlier, the one who had caused such pain for the space pirates, and for who he had been created to destroy. Though phazon gave him his power, it had destroyed his mind, making him little more than a beast, a powerful one, but a beast nonetheless. He was still was able to follow his missions, and one of his primary one was to destroy the Hunter. However, the second fighter was unexpected occurrence, especially due to the abilities it had possessed. When they met again, he would crush her slowly and painfully, strangling the life out of her until death took her in its cold grasp. Unbeknownst to him, however, he would never get that chance.
Hours beforehand, the Unit Omicron had arrived at the ruins. As they had begun to secure the phazon, a movement was noticed by their commander Rynoth. To their surprise, a clearly empty suit, resembling that of the Hunters, suddenly stood before them, held together by dark strands. Several of the elites began to open fire with their phazon weapons, unknowingly sealing their own fate. The suit began to absorb the blasts, and after a few moments, it began to laugh menacingly as its visor glowed a deep blue.
Raising its arm cannon, it shot the commando leader, obliterating him instantly. His squad mates slowly backed away in horror, and some even began ran. Aiming again, the suit fired several shots, each one striking a target. All five of the ATCs lifted off the ground after half of the surviving members boarded them, and they then began to open fire with everything they had. A massive cloud of dust was thrown into the air as their energy blasts and missiles struck at the spot the armor was standing in. As they cooled down after their weapons overheated, they waited to see the destruction they had caused.
Suddenly, phazon missiles burst out of the cloud of dust, knocking each ship out of the sky in a burning explosion. The remainder of the pirates began to flee once more, when suddenly the suit unleashed a powerful shockwave of pure phazon energy, incinerating them instantly on contact. Letting out another laugh, it suddenly felt drained again, having used too much energy in the attack. Stopping, it began to recharge itself on what remained of the units phazite armor, after which it knew it would only be a matter of time till it could achieve its goal.
The Omega reached the ruins with one finally burst of speed, toppling several pillars in the process. Looking around, it saw the signs of battle everywhere. Walking forward, crushing the charred bodies of several of its teammates beneath its footsteps, it eventually reached the large cylinder filled with phazon. Reaching in to recharge itself, it suddenly stopped as it sensed something.
Whipping around, it fired two phazon missiles at a ship that had been thrown at it. As the flaming wreckage slammed into the ground, it saw the living suit staring at it. Believing it to be the Hunter, it charged forward, roaring. Slamming its fist at it, he then began to pound the ground repeatedly at where he thought the Hunter was. As the dust cleared, he saw that there was no sign of the Hunter anywhere.
Looking around, it suddenly saw it floating inches from his own face. Swinging at it with his remaining fist, he thought he had it until the being caught his fist easily in its hand. Suddenly he was lifted off the ground and thrown into a nearby ship with relative ease. As he began to rise off the ground, he collapsed again. Suddenly, the figure appeared before him, and the last thing he saw was it placing its palm on his forehead, after which, the Omega exploded in blue flames.
In the distance, Samus and the others were still fallowing the trail of the Omega, which was a simple enough task due to all the destruction it had caused during its rampage. Samus began to ask Valfor how much farther away the ruins were when a massive column of blue flames appeared in the distance. Valfor said “I sense a dark presence, one I have felt before, but now it seems stronger.” Samus was about to question him what he had meant when they suddenly reached the ruins.
The area was littered with wrecked ships, broken weapons, and badly burnt pirate corpses. Dark Samus said “Could that thing have gone berserk and kill…” but stopped when she saw its massive body slammed against a crashed ship, its flesh charred as blue flames surrounded it. As she stepped backwards away from it, she bumped into the alter. Startled, she quickly turned around only to see her suit still lying upon it. Calming down, she called to Samus and said “What happened here?”
Turning to say something, Samus suddenly stopped as she saw the suit behind Dark Samus rise up. Suddenly sensing movement behind her, Dark Samus turned around just in time to be sent flying backwards by a whack of the suit's hand. Samus began to upon fire on the suit with everything she had, but it easily dodged every power beam shot at it. Samus then fired a super missile, but the suit grabbed it in midair before tossing it aside.
The suit then said, telepathically, in a sinister voice “We… meet… again… Samus…” before bursting forward with extreme speed. Leaping out of the way, Samus then began to open fire once again, hitting the suit several times in the back. Apparently unfazed, the suit turned around and said “You… will have to do… better than that… to win… this time...” before raising its own arm cannon.
It began to open fire with a barrage of rapid fire phazon shots. Samus started running behind a wall for cover as it crumbled from the attack. She then leapt out from behind it and fired a missile that disrupted the suits attack. Angered, the suit unleashed a wave of phazon energy that sent Samus flying backwards into the side of a shattered building. The suit screeched before charging forward, but was suddenly tackled by Dark Samus.
Samus slowly rose from the ground, her body in agony as Valfor ran to her aid. after which they then both looked towards Dark Samus. The suit was now hovering over the ground as it held Dark Samus by the neck. It said “Pitiful child… you chose to be weak and to betray me… to think my own daughter would do such a thing… when I regain my true form, you shall suffer my wrath.” Dark Samus seemed stunned as her face became solemn.
Tossing her aside, the suit proceeded towards the basin filled with phazon, knocking Valfor out of the way as he attempted to block it. It then hovered over the basin, and after facing Samus and the others, said “Foolish mortals, you all thought you could stop me from achieving greatness, from achieving power, from achieving my destiny. Now you shall face thy true form, a being with power beyond your comprehension.” With that, something glowing dropped off into the phazon, causing the suit to collapse in front of the basin, now resembling its original form, the phazon suit, though darker in coloration.
In space, Chitor’s flagship was taking massive damage from the planet’s defenses. One of Chitor’s techs alerted him that Samus’ location had been pinpointed. Hearing this, Chitor was overcome with feelings of anger for the damage she had done to his plans. He ordered the crew to open fire on the hunter. Meanwhile, back at the ruins, the basin of phazon began to bubble ferociously. Suddenly, laser fire bombarded the area, nearly hitting Samus and the others.
After the laser fire came near to hitting the basin, electrical currents began to ripple throughout the phazon pool seconds before a powerful beam of phazon was blasted out of it. On Chitor’s ship, one of the techs sudden yelled “Commander Chitor, we have detected a massive surge of energy coming from the planet, it’s going to… by the grand mother… it’s going to collide with…” The tech never finished his sentence due to the beam ripped through the ship.
Chitor roared “Keep us in orbit as long as possible! We cannot fail General Weavel!”
Meanwhile, back on the planet, the phazon had stopped bubbling. All of a sudden a massive entity burst from it, leaving nothing of the phazon in the basin behind. Floating before them was the powerful entity known as Metroid Prime. Staring at them intently, it gave out a sinister laugh before telepathically saying “I… AM… REBORN!”