Dr. Cain uncovered a strange capsule during a dig and immediately examined it. The device had been left behind by the late Dr. Light, and inside was the most unusual robot Dr. Cain had ever seen. “Mega Man X” could think and reason and do many other things that no robot could. Using X as a prototype, Dr. Cain built another robot, though he had to change a few things that he either didn’t understand or couldn’t duplicate. Even so, this new robot was far beyond anything the planet had seen, and quickly Dr. Cain put his new design on an assembly line, mass-producing these “Reploids” so that they could benefit humanity.


Dr. Cain, though an intelligent scientist, was nowhere near as brilliant as Dr. Light had been. He didn’t realize that he’d just created exactly what Dr. Light had feared: a race of robots that could think and make decisions, but that possessed no form of a conscience. With dangerous creatures like these, something was bound to go wrong.

And of course something did.

One of the Reploids attacked his fellow human workers, apparently having decided that robots were superior to humans. This Reploid was eliminated, but already others were coming to the same conclusion as the first. Scattered Reploids all over the planet were going “Maverick” and some were stopped only after heavy losses. Finally a Maverick Hunter squad was developed, with Dr. Cain’s best robot, Sigma, as the leader. For a while this squad kept the Mavericks in check.

Then Sigma himself went Maverick, and took the rest of the squad with him.

Mega Man X could not remember his past, and was unsure of his destiny. But he was determined to try to stop this force which he, indirectly, helped create. So he set out alone, one small robot among many, to deal with Sigma.

He didn’t even get past Vile.

Luckily a robot named Zero came to X’s aid. Now, the two stand alone against the hundreds of Maverick robots, with nothing but skill, luck, and Dr. Light’s capsules to aid them...

Setelah Zero mengorbankan diri untuk membunuh Vile, X langsung pergi melawan Sigma dan setelah pertarungan sengit akhirnya X menang melawan Sigma.
Berhasil keluar dari markas Sigma yang akhirnya meledak juga, X berpikir bahwa semua telah berakhir, tapi benarkah semua telah berakhir?

The Mavericks were thought to have been completely eliminated, but this was not so. X, the new leader of the Maverick Hunters, sets off with his fellows to eliminate the rest of the threating robots.

Eventually X discovers that though his partner Zero had destroyed himself to save his friend, his body still exists—though not in one piece. Three new robots—Agile, Violen, and Serges—use Zero’s parts like bait in order to lure X into his destruction. But if X doesn’t retrieve his friend’s body, to what horrible use will it be put?

Setelah berhasil menyelamatkan Zero, X langsung menerjang markas Sigma untuk mengakhiri semua, tapi didepannya telah menghadang sosok Zero, namun tiba - tiba Zero yang asli datang dan menebas Zero palsu tersebut, akhirnya konfrontasi X dan Sigma dimulai kembali, setelah berhasil mengahancurkan data Sigma yang menjadi virus, mereka berdua segera keluar dari markas tersebut dan menyaksikan markas itu hancur dari luar

X and Zero are partners once again, doing their job as Maverick Hunters. By now the Hunters have their own headquarters, apparently headed by Dr. Cain. The two Hunters discover that the attacks and raids by the Maverick robots are getting worse. Plus, more robots are going Maverick by the minute—even ones that had apparently been stable! Things really heat up, though, when the robotic scientist Dr. Doppler goes Maverick along with the others. Are the rumors of a deadly robot virus true? And if so, what would the world do if X and Zero were to fall to the virus too?

Dr. Doppler tiba - tiba sadar dan meminta maaf pada X karena terpengaruh virus dan membuat kekacauan di mana - mana, lalu sebelum dia meledakkan diri, dia memberi tahu letak Sigma berada dengan tubuh baru yang telah ia buat untuk Sigma, setelah X berhasil mengejar Sigma dan mengalahkannya, X dikejar - kejar oleh Sigma Virus dan terpojok sampai akhirnya Zero datang dengan membawa pedang Anti Virus , akhirnya Sigma tewas dan markasnya meledak seperti biasa

A group of reploids known as the Repliforce, led by Colonel and the huge General, desires independence from the humans that made them, although unlike the Mavericks, they do not wish to harm humans. Even so, a war breaks out between the Repliforce and the Maverick Hunters, who have pegged the force as Mavericks. And laughing as he watches it all from behind the scenes is, to quote Split Mushroom: “Take a wild guess.”

X pergi dari Final Weapon sambil mengingat2 kembali pertarungannya melawan Repliforce dan Sigma, tiba - tiba layar menyala dan Zero berkata "It's good to see you safe X." lalu X berkata "Zero, what if I become a Maverick?", Zero menyangkal pertanyaan itu dan akhirnya X berkata "Zero, if i'm become a maverick, you have to destroy me." setelah X berkata seperti itu Zero memutuskan komunikasi dan X akhirnya kembali ke bumi.

Zero pergi dari Final Weapon dan mengingat - ingat siapa saja Reploid2 yang sudah dia hancurkan hanya untuk mengalahkan Sigma, dia bingung berapa banyak lagi Reploid yang harus dia hancurkan untuk menyelesaikan semua ini.

Sigma attacks the Maverick Hunters base, then explodes, somehow managing to cover the entire planet with his virus with that one simple explosion (where’s the Maverick Hunter base again?). The virus causes most robots to go Maverick and sets the space colony known as Eurasia on a collision-course with Earth. The only way to stop it is to blow up the colony, either by building a powerful laser cannon to fire at it, or by building a shuttle and sending it on a kamikaze trip to crash into the colony.

Setelah X mengalahkan Sigma, Sigma meledakkan diri dengan Zero menyisakan Zero tinggal kepala, badan dan tangan kanan saja, X mengangkatnya sambil berteriak "Zero, Zeroooo...!!!" , namun dibelakangnya ternyata Sigma masih hidup, lalu menembak Zero dan X sampai tembus, setelah itu Zero langsung menembak Sigma dan akhirnya Sigma hancur, Zero berkata kepada X bahwa dia harus hidup, akhirnya X berhasil keluar dari markas Sigma namun hanya menyisakan kepala dan badannya saja yang hancur, lalu sebuah cahaya mendekatinya dan berkata "Not yet, you can't die yet." X dieslimuti cahaya biru terang dan akhirnya layar menjadi gelap . 3 Minggu kemudian, X bangun kembali dan akhirnya mulai melakukan pembasmian Maverick kembali, dengan tambahan pedang Zero di tangannya.

Three weeks after the crash of the space colony that almost obliterated the Earth, X is called into service once again to investigate the so-called “Nightmare Phenomena.” No one will say what exactly this whole Nightmare thing is, but it has to be stopped. Since Zero is missing and X is the only other Hunter worth his weight in salt, he’s assigned the job.

X menggendong Gate dan disampingnya ada Zero, Zero bertanya apakah dia masih terselamatkan, dan X menjawab sepertinya tidak, tak lama kemudian Alia, Signas, dan Douglas datang dan X meminta Alia untuk memperbaiki Gate, Happy Ending standar yg spesial untuk X Series

“Red Alert” is a new group of Reploids, similar to the Repliforce, only consisting more of vigilantes. They claim to hunt Mavericks, like the Maverick Hunters, but apparently they do far more than that. One of their members, Axl, decides he’s had enough of their “murdering” and so he tries to leave the group. Unfortunately, the group’s leader, Red, doesn’t take very kindly to this and goes on a mad tear to get Axl back.

When Axl finds his way to the Maverick Hunter base after stumbling across Zero, Red decides this means war and issues a challenge to the Hunters—he will release some Mavericks that Red Alert has in captivity, and whichever group can defeat the Mavericks first will win Axl.

So anyway, Axl wants to join up with the Maverick Hunters, and although X doesn’t grant this wish right away, the Hunters do allow Axl to fight with them against the Mavericks.

So it’s off to defeat the Mavericks, who have already taken root in various parts of the world...

In a rather cool cinema scene, X, Zero, and Axl have defeated Sigma, but he suddenly reappears and blasts Axl through a wall. Sigma is rather battered, but threatens to come back again in a stronger form. But before he can attack X and Zero, “Red” suddenly jumps down and assaults the Hunters, knocking them away. Sigma gloats then that he’ll take Red’s form; however, as he tries to do so, Red reveals himself to be Axl, and he shoots Sigma in the head so well that the single shot blows Sigma clean out of the tower. With Sigma taken care of, the trio heads home.

X Ending :
Back at HQ, Signas and Alia go through some reports of various Maverick “incidents” that Axl has stopped. (There were a few casualties though.) Anyway, Signas asks X if he will allow Axl to train to become a Maverick Hunter. X refuses, saying Axl could never become a hunter like him. Signas says that if X doesn’t fight, somebody else has to.

Zero Ending :
Zero has a dream of X pointing his arm cannon at him saying “Eliminate the Mavericks” over and over in a monotone. As Zero tries to ask what X is doing, X fires at him...and Zero wakes up. Alia is currently calling Zero for a mission, and Zero heads out murmuring, “At least, I hope that was just a dream...”

Axl Ending (yang ini blom namatin, kaset wa keburu pecah ) :
Axl wants to become a Maverick Hunter, but X still refuses. Axl says he was just doing what X was doing, but X says what he himself did was a mistake. Alia calls in a notice about a new Maverick incident, and Axl runs off, saying he’ll take care of it and that X will make him into a Hunter yet. Alia asks X why not just let Axl do what he wants this time. X says that Axl will make the same mistake they did. But Axl is already gone.

Earth is in such a turmoil due to the Reploid uprisings that humans have decided to colonize space instead. They’ve completed a project called “Jakob” which includes an elevator to the moon. Things go awry when Vile shows up and kidnaps Lumine, the Reploid director of the project. Sigma is therefore suspected of being behind the capture of the Jakob project. “Suspected” being the key word, since all next-generation Reploids are now equipped with Axl’s DNA Copy ability, and yes, as X discovers very quickly, some of them even went so far as to copy Sigma...

Lumine denies being Maverick and claims that the copy chips that the new Reploids have were derived from data from hundreds of old model Reploids...meaning Sigma was also included in the mix. Lumine also claims that Axl can’t go Maverick because he is only a prototype. Besides, he points out, was Sigma really crazy? He rebelled against the world but he had his reasons, or so Lumine thinks. Lumine adds that the new generation Reploids can go Maverick at will. Uh, that’s the stupidest thing I’ve ever heard. That’s like saying someone can go insane at will. Right...

Upon his death, Lumine declares that he may be defeated, but it’s too late to stop what has already begun. Then he goes still and starts to *****. Axl approaches Lumine, and some tentacles shoot from Lumine and hit Axl. Zero severs the tentacles with his saber while X catches Axl, then blasts Lumine.

X and Zero return to the orbital elevator with X still carrying a comatose Axl. Zero tells X to ignore what Lumine said. He says that even if this is the way all Reploids will eventually become, they will fight it every step of the way. They will fight their own destiny if necessary.

The game ends with a scene showing the cracked gem in Axl’s helmet, which Lumine shattered.

A robot named Techno has hacked into the Mother Computer at Maverick Hunter Base and is causing general mayhem and destruction. Naturally, X volunteers to dive in and put a stop to the madness at its source.

X destroys Techno’s computer, and Techno falls over, saying that since he’d connected his CPU to the computer, its destruction destroys him as well. Enter Middy, who reveals that he and Techno are twin brother, and since they share a CPU, , Techno’s fall will cause Middy to “die” as well. Sigma is revealed to have been controlling Techno and forcing him to do his bidding.

Reploids, powered by something known as a “DNA Soul”, cannot function without their souls. Someone has been going around gathering souls from Reploids to use in building items. Most of the Reploids attacked in this way merely deactivate. However some have had their souls replaced with the Maverick virus which naturally causes them to go Maverick. X and Zero have been called in to put a stop to whoever is behind this in order to save the Reploids from being deactivated.

X can sense the DNA Souls returning to the Reploids (evidently they just float back to their proper places on their own...unless they’re Maverick Souls of course). X also spends some time thinking about Zero. Although the game never mentions whether or not Zero succeeded in defeating Gareth without you, it is assumed he did.

It is the year 22XX.
A new mineral substance known as Force Metal has revolutionized Reploids. X and Zero, being Maverick Hunters, are sent out to a Force Metal facility one day to do their usual thing—that is, find and destroy a Maverick, this one named Epsilon. However, they are attacked by a large force and separated during the battle, and now X has joined up with some Reploids who are part of a resistance group, fighting back against a rebellion...

Redips and X’s team fail to see eye-to-eye. Redips doesn’t understand their concept of friendship and thinks that the Reploids will stagnate if they don’t continuously strive to increase their abilities and grow stronger. But the point is rather moot now, because the building they are in that had been in outer space is now heading for the Earth...with everyone still standing on it.

Ferham is still holding the Supra-Force Metal that she took from Redips. She asks X for permission to dispose of it herself, and he grants it to her. But, taking him by surprise, she then jumps off the building and floats off into space. When she’s a far enough distance away from the building and from Earth, she detonates, destroying both herself and the Supra-Force Metal.

Meanwhile, the building is tearing up as it reenters the atmosphere. X and the gang take cover inside. When they emerge later, they discover they have landed in the middle of the sea, and there is nothing but water all around them