This was outlined in the Notebooks a long time ago, but not written out, so I don't know if it counts as a Notebook Fic. Ties into/plays off of the 'Zero goes maverick' ending of X5, and has a couple alternate endings of its own, one being the game's outcome, in which Zero snaps out of it, then dies, and X doesn't remember Zero ever existed and won't remember anything he's told about him/won't accept data downloads either. Well, after X reappears post-rebuilding.
That could either be X repressing those memories because he can't live with them, knowing what he's missing without Zero (which is equally squee-inducing as carting around his beam saber so Zero will be watching over him/can get it when he comes back like in another ending), or something Zero did. X5's endings are even trickier to interpret since in the Inafune version you go straight from ALL THREE of them to Zero series (as X4's endings are equally valid) and in the X6+ version only one (not this one) is what actually happened.
In any case,
Disclaimer: I don't own Rockman and all other intellectual property referenced here. Capcom, Lucas, and the other rightful owners do. No infringement intended, no money made, please don't sue.
Zero didn't know who the speaker was, but he knew that he didn't want to. No, that he couldn't bear to, and that was frightening enough to give him a clue as to why.
"Do you want X to die?"
That was enough to force Zero awake, only to find that he couldn't gain any control over his systems. He could think, but his body was doing something and he had no idea what it was. Was this what it was like for those taken by the virus?
That was it. He'd lost to the virus, lost hope and…
"You're fighting X now, just so you know." And Zero could see, if only for an instant, that voice having far more control over his own systems than he did at the moment. "You can lie there and watch him die or you can fight." The vision of X dodging, his ex-trainee and partner so very conflicted, worried for him vanished.
"What can I do?" He hadn't been able to prevent the colony's fall, to do anything. This was all his fault.
"Nothing, with that attitude. Let me break things down for you." And Zero found himself in a virtual environment running on his own processor. A lab: he hated labs. "If things remain as they are, X will die. His odds of beating you and Sigma, one right after the other? Well, he's pulled off miracles before. But we both know why you didn't turn yourself in after the fourth war. With only one immune reploid the Hunters will have their capability cut to a third, and with you, who can create custom viruses, on the mavericks' side? Not to mention the atmospheric virus, the… the next war will be the last one if you don't wake up."
Zero couldn't argue, but, "Who are you?"
"Consider me a guide. Do you want to get control of your systems back or not?"
"You're wearing a black cloak and have a single eye under it. That's not exactly a look that inspires confidence." More like one that screamed 'bad guy.'
"We can't all be prettybots." He shrugged. "And you didn't answer the question. Are you going to just lay down and die, waiting for X to join you, because you lost one war? Your older brothers are all spinning in their graves like Topman."
Zero looked to the side. "Yeah, my family always lost in the end." The bad guys always lost, and Zero had tried to be a hero but, "I'm a Wilybot. X is the hero. I should just stay out of his way."
"And Protoman should have stayed out of Megaman's way. Let me rephrase the question. Do you want X to die?"And that tone demanded an answer.
"No matter how much of a defect you think you are, you have to admit that his odds of survival are better if you try to take your body back. Even if you're almost certain to fail that's a lot better than certain death. So don't throw yourself on the scrap pile just yet."
"I can't get my body back."
"Not like that, no. You wore yourself out in this war, not to mention letting yourself absorb virus since you needed the power increase, and one moment of despair weakened your self-control, or rather your determination to stay in control, enough it could shut you in here. You can't seriously fight it without more confidence or more power, although reminding you what you're fighting for," X appeared, a hologram between them, almost in the same pose, "helped."
"Why isn't he moving?"
"He is moving. You're an android master: Cain's OS might have limited you to the speed at which a human thinks, which normal reploids are limited to by the amount of ram, but your real self thinks in machine time. He hasn't slowed down, you've sped up, which is good because otherwise he'd be dead before you even got to work, at this rate."
X. "What do I need to do?"
"Well, finally. You can't regain control over your systems. You need to be able to access the systems Dr. Cain locked away, mostly by accident since he didn't know what they were, to have a fighting chance. Since they're locked away your original self, who Wily named Omega, can't use them either, which is part of why he hasn't won by now. He's not at all familiar with the fighting style he's currently limited to."
"So how do I unlock them?"
"You don't. There are a few key systems: virus control, weapon system control, defense control and mental control. There are people hanging around in your systems that you need to convince to unlock them for you. The downside is, if they do that they'll die, and for real this time."
"I have more split personalities?"
"No, call them ghosts. In the old days, robot masters didn't die when they blew up. Not if there was a backup station like this one." The shadowy figure that was starting to resemble death pointed to part of the scenery. "You know how Sigma doesn't stay dead. You have the ability to offer a safe haven for people you care about and were within range of when they died. You've done that for three people. However, it's not as simple for reploids since they have such bad designs. If they go against those systems' locks they'll use up all their energy, and since they only exist as electricity at the moment…"
"Who do you love more, a ghost or X? The past or the world's future?"
Hadn't he proven that by killing her? "Are you one of the three?"
"So you've come to tell me I'll be visited by three spirits and need to redeem myself if I don't want to be damned. Your name wouldn't happen to be Carol, would it?" He knew the virus' personality would finish him off eventually if he did nothing.
"It is nowhere near December and if you call me that I just might leave you to your own devices."
"Maybe Jacob Marley." Zero looked at him piercingly. "So you are a robot master, aren't you?" They'd often had musical names.
"To be more precise, I was a robot master. I'm one of the people you killed, just like Iris and the other two."
Not-Carol gestured to himself. "Isn't it obvious?"
Yeah, there was no way Light would build something that practically screamed evil. "So I really did kill everyone." Including his own family, own side.
He closed his eyes for a long moment. "No." Zero stood up, finally, from where he'd fallen. "Omega did."
"If you say so." The cloaked figure was surprisingly short when he stood up.
"Take me to Iris."
"I doubt it will come up again, but given the second law it is incredibly rude to give orders to robot masters. You're not a human and Wilybots that were built by Wily himself never had the laws, but everyone else had to get around it constantly and it was a very annoying pain in the processor. 'Go jump in a lake' is the classic example. Not to mention that you're going to be asking people you've murdered for favors."
"I'm sorry." Zero was.
"Apology accepted." Now rephrase that.
"Why are you helping me?" For all he knew this was something to do with the virus.
"X has those holograms of Dr. Light: you have me."
"I killed you and Dr. Wily forced you to look after me?"
'Jacob,' as Zero had decided to call him, laughed. "The things we do for family. Now, don't you have something to do?"
There was no choice, was there. "Please take me to Iris?"