If we're to avoid the simple conclusion that Capcom and Inti's concept about what the virus is and does have simply changed over the years to the point where the old sources are obsolete outright...
I wrote this sometime last week, so it doesn't apply to all the previous discussion in the thread, but maybe it can further discussion. There's so many cluttered and contradictory ideas that the virus is supposed to satisfy, that I had a difficult time keeping it all orderly in my head. So I used lettering and numbering to try and organize my thoughts better, and also make arguing each single point a little easier.
Observations:
A. Zero was "bad" before Zero was "infected." (ZC Timeline)
B. Zero was armored against the virus. (ZC Timeline, also possibly corresponding to the various references to virus immunity)
C. Zero's DNA contains the virus program. (X6, X8)
D. Zero's power grows from virus exposure. (X5)
Hypothesis:
1. Zero was built to protect his mind against the virus. His DNA program contains information about the virus (perhaps a "core" piece of the virus code itself) to allow his automatic systems to recognize it and disperse it safely without doing harm to his cognitive program. Zero's body redirects the "energy/volition" of the virus and channels it into his power output, temporarily boosting his power.
Observations:
E. Zero's capsule emits the virus. (ZC)
F. Sigma broke through Zero's armoring and Zero got infected. (ZC, visually X4)
G. Zero's personality changed due to virus infection. (ZC)
H. The virus can cause the resurfacing of the latent evil personality within Zero (X5, visually X2).
I. The virus can cause aggressive and violent behavior in normal robots. (ZC, R10? all X series?)
Hypothesis:
2. Zero's damaged armor allowed the Virus to bypass his defenses (H-1) and enter Zero's cognitive program directly, causing...
2a. ...Zero's already heightened levels of negative emotions to overload and crash, resulting in a "blank slate" mode with bottomed-out aggression levels. Further virus infiltration can restore the emotional negativity to higher levels, but his body's defenses were restored and resumed their functions of virus suppression. Zero's defenses can be bypassed by access to his brain directly, or become overwhelmed by more virus than it can safely expel.
2b. ...a rewrite to the thought program by reversing the 'default' output levels for aggression checking, like turning a 0 to a 1. In Zero's unique case, because the aggression levels were already full by default, reversing the code caused the violence to recede. A different strain of virus might need to be tailored specifically to Zero to properly undo this effect, but this different virus would need to get past Zero's defenses to do so. Zero's defenses can be bypassed by access to his brain directly, or become overwhelmed by more virus than it can safely expel.
Observations:
J. Zero is a virus carrier, and spreads the virus while working as a Hunter. (ZC, MZOCW, X6's Gate)
Hypothesis:
3a. Zero now has active virus infection (H-2a) in his brain which tries to copy itself and spread, but at the same time his body's defenses try to disperse the new virus even as it is made (H-1). At a time when Zero is acting aggressively and exerting high energy levels, like with battling with mavericks, his aggression creates copies of the virus which his body draws upon and expels, releasing virus to the surrounding environment.
3b. Zero's armor protects him from outside infection (H-1) but the infection already within himself (2b) occasionally builds up and leaks out. This can also occur if Zero's armor is damaged and his infected insides are exposed.
Observations:
K. The virus can revive the dead. (Ask Inafune, Sigma in X6)
L. The Sigma Virus is considered a kind of Cyber Elf. (ZC)
M. There exists a Cyber Space dimension where all functions of the physical world are manifested as data. (Z3, Telos booklet)
N*. Under certain conditions, rifts into Cyber Space can be created, causing anomalies. (*Conjecture based on X5's Zero Space, X6's Nightmare stage effects, Z3's Cyber Space Doors, ZX's Area M/N)
Hypothesis:
4. The virus, as a cyber elf, exists as a form of bridge between the dimensions of physical space and Cyber Space. Large concentrations of a powerful virus can (perhaps when combined with other factors) create overlaps where data from Cyber Space is brought into the physical world. The virus can be specifically utilized to draw the volition and memories of a departed soul's data back to the world of the living to be resurrected, either by complete error or by direction from someone with the knowledge and resources to do so.
Observations:
O. Wily had a side project in addition to his Zero project. (PF)
P. An ancient virus from space is the basis for the current Sigma Virus. (ZC)
Q. Rockman 10 contains a "threat from outer space". (R10 subtitle)
Hypothesis:
5a. Wily's side project was his creation of the Roboenza Virus, which he spread from his space station. After R10 Wily gave up on using it and stored his leftover virus in the same facility as Zero, where it eventually mutates and starts to spread through the facility and leak out through Zero's capsule, and incidentally brings Wily's data back from the dead.
5b. Wily's side project was a perfect form of the Roboenza Virus, which he continued to refine until his death for use in a new master plan to utilize it in conjunction with Zero somehow. That the virus brought him back from the dead however was unexpected.
5c. Wily's side project was a way for himself to cheat death, eventually using some form of the Roboenza virus as a centerpiece in his plan. Wily recognized the virus' potential expanded much further than just manipulating robots. He intentionally used the virus to resurrect himself upon his death.
I have a feeling these hardly scratch the surface of all the variant pieces of information that need explaining, and all these hypothesis, especially where they build off each other, may be well off the mark. For instance, I didn't really explore the nature of Zero's body changes and possible effects it could have on Hypothesis 1-3. I just wanted to establish at least one way where it might be possible to put it all together into a complete picture. I'll leave it to you guys to pick it all apart.
Reading through, I like some of the ideas in this thread. The virus being inside Zero's capsule to perform some kind of testing, that Wily just didn't shove Zero into a capsule to get rid of him, but to try and bring him around. And the virus perhaps increasing Zero's emotional coldness, where it seems to make everyone else more hotheaded. And that the "W" could still be something outside of the virus infection. I do think Wily has some manner of communicating with Zero during Zero's subconscious states, but I don't think we've ever seen a "W" appearing on his head in any time other than that one instance. But maybe that's because it's never been as strong again since that time.
Perhaps Sigma gets infected by the capsule, but also receives some of Zero's DNA with the immunity in it during their fight, allowing it to infect him uniquely as well? That might satisfy both seemingly contradictory notions about where Sigma's virus came from, but I have doubts whether it's not supposed to be one or the other.
I'll repeat this from our last supra-force argument, because it sounds like still nobody read it:
Sigma in the Japanese version of X5 reflects that Awakened Zero was indeed complete, in personality anyway.
しんのすがたにもどれたのに...ゼロよ。ごくろうだったよ。
"Even though your true form had returned... Zero. Thank you for all your effort."
It's possible that Zero was able to increase his power during the course of the battle, but the evil persona was in place since the Shuttle Mission failure. Hence "Awakened" Zero, not "Awakening" or "almost Awakened."
Sigma finding Zero's evil form incomplete is a poor translation thing.
Moving on, the idea that the capsule was spreading the virus but was not what infected Zero really perplexed me. From my memory, there didn't seem to be much in the way of extraordinary about the capsule other than that Zero was sleeping/being constructed in it. I wanted to go back and see if there were any clues that the capsule was connected to the virus or leaking anything. It could all be a wild goose chase, but here's what I found.
Zero's capsule, with him in it. Since we've been told Zero wasn't sealed until after he was built, we might say that this is his version of the diagnostic/testing phase.
Zero waking up from the capsule, both seeming roughly undamaged from what can be told.
Capsule opened, and empty. After Zero left?
Inside the capsule, Wily visible. This is from the intro/dream sequence instead of the ending. Is this directly after Zero's sealing, or before waking up? I never noticed that Zero's legs were colored wrong before.
So I didn't find much in the way of visible damage to the capsule itself. But there are those cords coming from Zero's capsule in the first shot where we can't see what they're connected to.
Could they be connected to this? Some kind of tanks. The one glowing purple doesn't seem to be connected to the wires, but maybe it's just hidden. The symbol on there is like a radiation warning symbol, except with 5 parts instead of 4. The only other place I remember seeing this symbol was in Zero 1's intro stage, but I don't think it's even visible without using an emulator or cheats.
Could this be some sort of hazardous symbol for robots? If related to the virus, does that make that a virus holding tank? Maybe the virus leaks out from these, or from the cable connections? Maybe there are two types of virus being held here?
Looks like the cables might be going to Zero's head... of course, they could be completely unrelated cables.
The only other thing I thought might be significant, the three tube-looking containers on the right side of this picture. They vaguely remind me of the way the three huge containers in Wily's space station in R10 look, although those aren't explicitly said to be virus containers. It looks like there's yellow and purple substances mixing inside them, sort of like the yellow and purple lights on the tanks. It might be nothing, or might be something.