Author's Note: This is my take on a story of Mega Man X9 if Capcom decides to make it, I don't work for Capcom and I don't have a Degree on Literature, I'm gonna try and not spoil the ending of X8 if you want to play it for yourself so here we go.
Now the story begins with X and Zero returning Axl back to base, when they told the news something was haunting Zero for a long time, he informed the Maverick Hunters that a voice keeps saying that he's the most powerful Reploid around, so Zero decided to go find the truth of his past, X decided to visit his creator Dr. Light's Ruined Lab to pay his respects to his creator as well.
When X started off Alia contacted X "X are you sure you want to revisit your past." X was absolutely sure, "I'm sure, if Zero is gonna find out about his past, then I am gonna find that last message my creator Dr. Light recorded." Alia then said "Alright, X be sure to be back once you're done." X then said "Rodger that." Alia then said "Umm X?" X was curious "What is it Alia?" Alia stopped herself for a moment "Never mind X, good luck."
As he went to the ruins of Dr. Light's Lab, he visited his creator's grave and said "Dr. Light, it has been a long time, I always hoped that Reploids and humans would live in peace, however, something gone wrong and many viruses have caused them to go berserk and we now call them Mavericks, Forgive me Doctor, but I might not see the light of day once that day comes."
Meanwhile Zero was unsure if he is gonna like what his origins were, "Zero." Layer said "This is a bad idea." Zero then said "I know, but it's the only way that I can learn the truth about my past, Sigma, Isoc, that man, they said that I'm the strongest creation, Sigma tried to turn me Maverick Twice, and I'm gonna find out why." Layer then said "Alright, I won't stop you, I hope you come back in one piece." Zero then said "I will, Thanks Layer."
When he made it to the ruins of Dr. Wily's lab he said "What happened here?" He went in to investigate, when he went in he was shocked he had a horrified look on his face, and he saw a bunch of Robotic Corpses, he asked himself "Who did this? What I remember is that man, nothing else...X, Colonel, Iris, Axl…"
Meanwhile in the ruins of Dr Light's Lab, he looked at a video drive, he contacted Alia "Alia, I found something." Alia then said "What is it?" He then said "It's some sort of drive, I'm getting a recording of it." He inserted the drive and a recording of an old Dr. Light with his final message "Greetings X if you are watching this you already know about your purpose in life, but there is someone else who has a last creation, Dr. Albert Wily, he was my old friend now sworn enemy, my helper robot Mega Man has stopped him time and time again, I wished things were different, and I hope one day that the world would be in peace, but now I can't see that happening today...you're our only hope X...one day you shall fulfill my wish...goodbye…X…" then he perished, he saw there was still more.
"Doctor, I'm sorry." He fast forwarded the recording he saw a Helper Robot, "X, don't be alarmed, I'm Rock, AKA Mega Man." X didn't say a word "Mega Man?" He continued watching the video "X don't go any close to Dr. Wily's nasty creation, he's far too dangerous, once you become stronger challenge him and destroy him, it's the only way for peace, I might not survive so long to see you since Dr. Light is the only one who can repair me, I'm sorry I might not make it in 100 Years, Neither would my sister Roll, my brother Proto Man, or my rival Bass, I'm counting on you little brother." X turned off the video and said "Who is this Dr. Wily?"
Meanwhile Zero looked through the files and looked at a drive about his creation, and popped it in the computer and once it was done loading, he saw footage of his dream he kept having, it was real, he fastforwarded it to see more information, but there was nothing else, he kept looking "Where is something that knows about my past." and then looked at the drive of the final words of Dr. Wily, it was a Suicide Note "What is this?" He popped it in and it loaded up and it said "Ah Mega Man, it is I Dr. Wily, As it turns out, I am not even here, You'll never see me alive again, you will be destroyed by my greatest creation, Zero." Zero was horrified, of what he heard "So…He's my…" he said "Once Zero destroys you, and whatever is left of Dr. Light, the world shall see that he will fulfill my wish to take over the world, farewell Mega Man!" Wily said.
Then Dr. Wily turned off the recording, and Zero trembled and said "Did I Do This?" Zero had a call from Layer "Zero, What's Wrong?" Zero pretended he was being serious said "Nothing Layer." She then said "Did you find anything?" Zero then said "No, I'm coming back to base." He hung up, and said "I must not tell anyone about my past, or else no one is going to trust me again."
Author's Note: This idea popped into my head, X knew about his past when he was being built by Dr. Light, but Zero never knew, so I'm picturing what will happen if Zero found out about his past.