I don't remember that part...
Get equipped with the Zero-collection official site timeline.
It may just be my crappy memory, but I don't think I've heard anything about that "Three Keys" bit; what was the Udon translator's interpretation?
Marshmallowman's translation:
Sigma Virus
The dreadful Sigma Virus that transforms Repliroid to Irregular.
The true form of which, was a suffering circuit Right inserted into X during the time of his creation.
A Repliroid which possesses a suffering circuit,
in regards to a society where humans and Repliroids coexist,
so as to be biased towards neither side,
it is fated always to worry continuously as to which side it should stand upon.
Zero was the first Repliroid to be infected with the Sigma Virus but
Zero which was developed by Wily to be a completely evil Repliroid,
despite being infected by Sigma Virus isn't transformed into an Irregular, [instead]
was reborn as a good Repliroid.
But,
as Zero bustled about for the sake of fulfilling his missions as an Irregular Hunter
the Sigma virus lying dormant within his own body was scattered throughout the world
inviting an ironic result.
And so Zero, having become carrier of the Sigma Virus, was admitted to the research facility.
***
Udon's localization:
Sigma Virus
The terrifying virus that causes a Reploid to go Maverick. The virus actually originated from one of the circuits that Dr. Light installed in X's brain. The circuits function was to keep X neutral and unbiased in matters concerning humans and Reploids. Tragically, the very same circuit condemned X to a life plagued by the philosophical question that weighed the value of humans against that of Reploids - a question to which there was no answer. Zero was the first Reploid to be infected by the virus, but as an android created solely for evil, destructive purposes by Dr. Wily, the virus affected him uniquely. Instead of going Maverick, the virus turned Zero into a warrior driven by goodness, not evil. Unfortunately, by tirelessly fulfilling his destiny as a Maverick Hunter, Zero inadvertently spread the virus throughout the world. Eventually, as the host of the virus, Zero was taken to a research facility for study.
***
Key differences exist in the beginning; Udon's localizer added details to the circuit - virus relationship that's not at all explained within the original text. After which, explaining the regular function of said circuit in Reploids, Udon removes the mention of Reploids in general, replacing it with just X.
Udon's interpretation of the circuit - virus relationship was eventually proven wrong by the ZERO-collection official site. The latter half, concerning Zero becoming good by the virus, was proven by that same site, but prior to that was not as unambiguous as Udon makes it out to be; without the additional explanations given, it seemingly went against all established fact.