August 17, 21XX: "These new hover bikes you invented are great Dr. Cain," Mega Man X excitedly reports.
"Excellent design," Zero adds nonchalantly, "exceptional maneuvering, superb acceleration."
"Thank you for that glowing report," Dr. Cain responds sarcastically. "How do you think they'll do the next time Sigma attacks?"
"Great" "Sufficient" the two reploids answer simultaneously.
"Good," Cain starts, "I'll start construction on more, the two of you go through equipment like nobody's... hold on. We have a report of a maverick attack at [Static] Park, and [Static] power Plant [Static] like [Long break of static] dead?" by this point the transmission has degraded beyond redemption.
"Zero, you head for the Power Plant," X orders, "I'll head for the City Park" Zero nods his agreement and vectors off towards the plant.
As X arrives he gets shot by a spiral of fire arcing towards him. X is thrown from his bike as another maverick jumps towards him and kicks him in the chest. He's about to fire when a third fires an EMP Cannon at him knocking him to the ground. Before he can get up another one fires a pair of plasma blasts at his arms, pinning him into submission. While trying to get up a shadow comes over him and says: "so this is the famous Mega Man X. I must say I'm not impressed."
Meanwhile, at the city's nuclear fusion power plant Zero surveys the area trying to find the reported maverick. "I'm right here Zero," he hears from right behind him. He quickly turns around and sees a reploid of similar height as himself.
"Who are you," Zero demands.
"My name is Time Man," the reploid begins, "and like you I am a creation of Dr. Wily."
"Maybe, but Wily's been dead for decades," Zero explains patronizingly, "I should know, I killed him."
"True," Time Man grins, "but it takes more than a little thing like death to stop an evil genius like Wily."
"I may have been created by Wily, but that doesn't mean I'll help him!" Zero growls through his teeth.
"Then you shall die!" Time Man says readying a weapon. Zero is about to move when he's hit square in the chest. He then sees the weapon being fired. "I'm not called Time Man for nothing," he explains smiling. He then teleports away.
X finally gathers up enough strength to look up and sees the legendary visage of Dr. Wily. "Wily?" X asks weakly, "I thought you were dead."
"I get that a lot," Wily jokes. He then turns towards his army of Robot Masters. "We have to go." And as quickly as the battle began all of them were gone. Leaving X alone wounded and confused. As he limps towards his crashed, but operational, Hover Bike he receives a transmission.
"X, this is Zero," Zero begins, "I'm at the power plant. The reactor's going critical, and I can't stop it. The radiation is interfering with my teleporter. Everything within a hundred kilometer radius is going be destroyed. You have to move X."
"Zero," X starts desperately, "you gotta get out of there!"
"There's not enough time for me. I'm sorry. But, you have to move NOW!"
"X, move!" an unknown voice sounds within X's head.
"Who said that?" he asks.
"We don't have time for games X, GO!" Quickly X gets on his bike and takes off for Maverick Hunter HQ. He barely gets out of the blast radius in time to avoid being incinerated.
After a brief resupply, X heads after Wily's New Robot/Reploid Masters. First to be defeated is Dual Man. After that the skillful Ninja Man. Following that is Flame Man. Then he goes after Image Man. Ion Man is next.
He then goes after the mysterious Crush. When he arrives, before they fight Crush says, "So you're Mega Man X. I don't see what the big deal is."
"You don't act like Wily's other mavericks," X begins, "what makes you so different?"
"Nothing gets by you X does it?" Crush asks sarcastically, "it hardly matters though." At this point Crush opens fire on X.
At the end of the fight Crush asks, "If you're having such a hard time beating me, what makes you think you could ever defeat Wily?" After asking this Crush teleports out, leaving the Crush Beam behind.
After this odd fight, X goes on to fight Time Man, the last of Wily's Robot Masters. He then goes after Wily's New Scull Catle. After getting through the front gate area an exact copy of X attacks him. X is able to defeat him easily. Afterwards a pair of energy bindings come down. One attaches itself to X, and the other to Nega Man. Nega Man reactivates and attacks again. This time X barely emerges victorious.
After fighting his way through the rest of the New Scull Castle, X finds himself face to face with Dr. Wily. Wily looks at him and says, "I've been expecting you 'X' is it? Anyway, I must say I'm disappointed. Your predecessor would have made it here hours ago."
"Enough talk," X growls through his teeth, "I'm here to bring you to justice."
"But I don't think it's justice you want X," Wily points out and then whispers, "I think you just want revenge for Zero." X doesn't answer, he just attacks with unchecked rage.
After the brief fight Wily lies on the ground with X standing over him. "Please forgive me!" Wily begs, "I won't fail you again! Please forgive me Sigma!"
"Sigma?!" X asks in disbelief.
"Wily you sniveling worm, why did I ever think cloning you was a good idea" Sigma spits emerging from the shadows, "must I do everything myself?" he asks as he blasts a still dumbfounded X with a shot so powerful the building starts to collapse. "Let's go," he orders his human partner.
Hours later when X reawakens, he clears himself out of the rubble with many questions. "Sigma working with a human? I thought he hated humanity. Well, then again, so does Wily." At this point he receives a message from Dr. Cain.
"X," he impatiently begins, "just what the HELL is going on?"
"Sigma and Wily have appeared to join forces," X explains weakly.
"Isn't Wily dead?" The human asks confused.
"That was my first reaction," X smiles grimly, "as far as I can tell Sigma cloned him."
"If Sigma cloned Wily, that means that he can be cured!"
"What!?"
"X, come on you should study your biology and history more. About a decade after Wily's death a cure for the mental instability that affected him was found. Head to the lab and we can give you the vaccine, it's a part of standard medical supplies."
"Oh," X begins a little ashamed, "maybe I should have mentioned Wily sooner. Anyway," he tries coolly, "I'll head over to the lab. See ya soon. X out."
After getting the vaccine X heads after Sigma's mavericks, Armored Beetle, Freeze Ferret, Disintegration Dragon, Gravity Raven, Stellar Scorpion, Juggernaut Rhino, and King Cobra. After the last maverick is destroyed X goes after Sigma's fortress. When he gets to what he named "the boss room," a familiar looking maverick is waiting for him.
"Zero?" X asks in disbelief.
"No," he begins, "I'm not Zero, X. I'm Null. Wily built me after Zero failed to perform his duty, of destroying you!" And with that Null attacks X. Battered, X emerges victorious, barely.
X then continues after Sigma. Once there, a long battle ensues. Both combatants appear to be evenly matched. X finally gets in a lucky blow and cripples Sigma. At this point Wily appears and escapes with Sigma before X has a chance to hit him with the dart full of the vaccine.
X learns of a new fortress, designed by both Wily and Sigma. X immediately goes after it. Inside he fights clones of all of the mavericks he already fought. He eventually makes his way to Wily. X first has to destroy part of the machine Wily is fighting in before he can hit him with the vaccine dart. When he finally succeeds, Wily just lies on the ground. Sigma then shows up and attacks. This battle is very one sided. As Sigma is about to destroy X, Wily attacks Sigma, destroying him.
X looks at Wily confused. Wily returns the look. "Rock?" he asks, "is that. No, you're not Rock, you're... 'X', right? It's all a little blurred together. The last thing I remember clearly is being in the lab with Thomas. Wait!" he shouts running over to the computer. He presses some buttons quickly before X has a chance to ask him what he's doing. "There, I just deleted Sigma once and for all. It's the least I could do after... what I did. X, I know you don't trust me yet, but you should follow me."
Cautiously X does as instructed, with his X-Buster at the ready. Wily leads him to a special chamber. "While under the 'leadership' of Sigma, I created a clone of Thomas, Dr. Light. I'm going to undo the reprogramming we did to him. Hold on." He finishes grabbing a piece of medical equipment. After a few minutes of playing with the innards of Dr. Light's head, he succeeds.
"X?!" Dr. Light asks astounded, "is that you. But, you weren't supposed to be activated until after I died."
"It's okay Thomas," Wily assures him.
"Albert?" Light asks, "I was at your funeral, what's going on?" Wily proceeds to tell his old friend about everything that happened since his 'rebirth' decades after his death.
As the two walk off X realizes that the effects of Sigma's tampering with genetics are far from over. "Good job X," the voice returns.