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Episode 5 of the X series is written below from X's perspective. Because of the games' multiple endings, use the guide below to navigate without ruining the story for yourself.
Prologue
Intro
Enigma Success
Shuttle Success
Shuttle Fail
X's Ending
Zero's Ending

Prologue (Taken from manual):
The year is AD 21XX... The galaxy is at peace after centuries of fighting the Reploid Wars... The moon is the center of a swarm of orbiting space colonies. The largest, a massive colony named Eurasia, is undergoing extensive renovation to make it the most colossal and most advanced of all the orbiting outposts. When an unknown evil force occupies Eurasia, the peace collapses! Eurasia's artificial gravity device is wrecked. The colony spins out of orbit, and is now headed on a collision course towards Earth! The outpost will hit Earth in 24 hours. If they collide, Earth could be totally destroyed. It could even vanish! The only way to shield Earth is to deploy Enigma, an ancient particla cannon left over from the Reploid Wars. The future of the planet is entrusted to Mega Man X and Zero. Can they save the planet?
Next

Into the game with X:
X rushes to the last coordinates where Zero was heard from, with Alia guiding him. When he enters an empty room, Zero teleports in with his Z-Buster damaged. Pretty soon, Sigma appears, but X easily defeats him. Meanwhile, the colony has been leaking out a virus. Sigma purposely lost as a diversion while the Maverick Virus spread throughout the Earth, and the colony plummeted towards it. The only way to stop it is to deply Enigma, an ancient particle beam. For it to work, Douglass requests that you find 4 parts to strengthen it; The Crystal Ball from Grizzly Slash, The Orifalcon from Squid Adler, the Laser Device from Izzy Glow, and Hydrogen from Duff Mcwhalen.
Enigma Success
Enigma Fail

Enigma Success with X:
After getting all 4 parts and deploying th Enigma, the colony is destroyed and peace is restored. But the colony virus seemed to have bonded with the Sigma Virus on Earth, creating a new virus, which Alia named: the Zero Virus. Also, a strong energy signature was detected, which was no doubt Sigma. To reach him, X has to fight through the , the newly enhanced Vegaulder, and the 8 Maverick Bosses. Defeating them was no problem, but after clearing a path to victory, X found himself staring at Zero in an empty room. Zero tried to take over X's mission, saying that he could handle it. When Zero refused to return to base, X had to fight him for his sake. The result ended with both of them worn out. Suddenly, Sigma appeared, ready to finish off X. But Zero jumped in for the save, and drove him off, which only prolonged their confrontation.
X, after finally reaching Sigma's coordinates, found himself fighting the very cause of the whole problem: Sigma. Defeating him proved no simple task, but he managed to dodge energy wave after energy wave until is nemesis was destroyed. But as seen before, Sigma always comes back in a 2nd form. This time, a gigantic version of himself attempted to crush X, by smashing his hands together, shooting plasma blasts, and energy rings. X only barely destroyed him.
Ending

Enigma Fail with X:
After launching the Enigma, it only destroyed part of the colony. The backup mission is the Shuttle Mission. The plan is to send someone on the shuttle, pilot it towards the colony, and crash it into it while escaping. To strengthen the shuttle, Douglass needs 4 parts.
Shuttle Success
Shuttle Fail

Shuttle Success with X:
After getting all 4 parts and launching Zero to the colony, it is destroyed, and Zero returns safely to Earth. But the colony virus seemed to have bonded with the Sigma Virus on Earth, creating a new virus, which Alia named: the Zero Virus. Also, a strong energy signature was detected, which was no doubt Sigma. To reach him, X has to fight through the, the newly enhanced Vegaulder, and the 8 Maverick Bosses. Defeating them was no problem, but after clearing a path to victory, X found himself staring at Zero in an empty room. Zero tried to take over X's mission, saying that he could handle it. When Zero refused to return to base, X had to fight him for his sake. The result ended with both of them worn out. Suddenly, Sigma appeared, ready to finish off X. But Zero jumped in for the save, and drove him off, which only prolonged their confrontation.
X, after finally reaching Sigma's coordinates, found himself fighting the very cause of the whole problem: Sigma. Defeating him proved no simple task, but he managed to dodge energy wave after energy wave until is nemesis was destroyed. But as seen before, Sigma always comes back in a 2nd form. This time, a gigantic version of himself attempted to crush X, by smashing his hands together, shooting plasma blasts, and energy rings. X only barely destroyed him.
Ending

Shuttle Fail with X:
Getting the 4 parts wasn't enough to destroy the colony, and it crashed into Earth. Mankind barely survived the impact, and are living underground until the reploids finish renovating the Earth until it is fit for living. X rushes to go find Zero's escape pod, and when he reaches there he find a mysteriously powerful energy aura. The owner of that energy aura was Zero, who floated above X and challenged him to a fight. In order to save his friend, X accepted. Before he could, though, 2 challenges awaited him; a black sludge maverick and a newly upgraded Rangda Bangda. Defeating them proved to be no simple task, as they were stronger than before. After finally dealing with the enemies of the past, X found himself fighting one of the fiercest battles of his life against non other than Zero. The Sigma Virus seemed to have strengthened him. After a long fight, both collapsed on the floor, exhausted and drained of their energy. Suddenly, Sigma appeared before them, and tried to take out the unconscious X. Zero jumped in and drove Sigma off, leaving yet another opponent for them to battle. Before Sigma, the previous 8 Mavericks arrived, but X was able to easily destroy them.
X, after finally reaching Sigma's coordinates, found himself fighting the very cause of the whole problem: Sigma. Defeating him proved no simple task, but he managed to dodge energy wave after energy wave until is nemesis was destroyed. But as seen before, Sigma always comes back in a 2nd form. This time, a gigantic version of himself attempted to crush X, by smashing his hands together, shooting plasma blasts, and energy rings. X only barely destroyed him
X's Ending

Ending:
But before he died, Sigma took Zero with him.
With his body torn in half, Zero clung onto dear life. When X rushed over to check his friend's condition, Sigma, with his last breath, shot an energy beam at them. It piered both reploid's bodies, leaving a hole in both their chests. Trying to save x, Zero used the last of his power to finish off Sigma. With no energy left, the life ran out of him.
X, meanwhile, was dying fast, until a mysterious spirit appeared, and nursed him back to health. 3 years later, a maverick was spotted, and Alia alerted X, now a captain, to bring the new Hunters to solve the problem. Now carrying Zero's old beam saber, X rushes into battle, never forgeting his brave friend.

2nd Ending:
But before he died, Sigma took Zero with him.
X was caught in the explotion, with only his upper torso left, when a mysterious spirit appeared and healed him.
1 week later, X was talking to other fellow Hunters, when Zero was mentioned. X had no memories of this person, or anything that involved him. Alia, Signas, and Douglas were relieved that X came back without a scratch. X and Zero's bodies were not analyzed before, so they couldn't repair each of them. They were relieved they did not have to deal with X's injuries. A mystery still remained... who had deleted X's memories? And more so, why were only memories of Zero deleted? And so X lived his days not remembering his savior, and best friend...

Zero's Ending:
Right before Sigma launches a final attack to defeat X, Zero jumps in and musters enough energy to destroy Sigma for good. With his energy drained and systems heavily damaged, Zero clings onto dear life. His memory chip seems to be malfunctioning, as old memories come back to life. A glimpse of Iris... his first battle with Sigma... a mysterious old scientist... all of them run by his mind one last time, as his eyes close and his system shuts down...

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