It's no doubt that I think Sigma is the best Megaman franchise villain ever. I feel he's more developed than all the villains such as Dr. Wily (for the Classic series), the Bonnes (for the now-defunct Legends series), or any of the other villains that were conceived for any Megaman entry. Now, a plot was seems to be either forgotten or somewhat played with is the plot that his true form (that is, according to Dr. Doppler) is a computer virus.
TV Tropes has this rather interesting point about him:
Dead All Along: Neither X nor Zero ever were made aware, but X4 and Word of God clued in the audience that the "Sigma" who incites war throughout the series isn't even the genuine article. Commander Sigma, the Maverick Hunter, ceased to be when he first encountered Zero, long before the series even started. His consciousness was overtaken and assimilated by the Maverick Virus, causing it to mutate into the Sigma Virus, which walked around in his body until X first destroyed him.
So, it seems that the later plots don't contradict. Dr. Doppler is most likely correct to say that Sigma's true form is that of a computer virus. Megaman X2 has Sigma reveal his form as a virus and it's banished. In Megaman X3, Sigma would later become a virus after he's defeated (resulting in the most tedious Sigma battle ever) and try to possess Megaman X's body. Dr. Doppler uses an anti-virus yet he manages to return in Megaman X4 in the form of the Grim Reaper. He does manage to keep returning but is apparently gone for good in Megaman X8. In Megaman X6, you can see the virus in the dialogue box which implies that he wasn't truly vanquished but the program is still not fully restored.
The back-origin story in Megaman X4 could actually provide an explanation. If you're playing as Zero then be ready for a more interesting blast to the past. Zero's origins are verified that he's Dr. Wily's masterpiece and supposed successor. Yet, Sigma became that successor. The flashback reveals that Sigma was probably once that selfless, well-admired Maverick Hunter. However, the battle with Zero unleashed the Maverick Virus into Sigma. Sooner or later, the virus entered into Sigma's body and created the Sigma Virus. Probably, this resulted in the deletion of the original Sigma program. So, whatever was left of Commander Sigma is gone. However, the Sigma Virus may have copied whatever memories the original Sigma had creating a bizarre amalgamation. It seems that the Evil Energy in Megaman 8 was used to create the Maverick Virus, it did gain sentience merging with Sigma's data, and the original data of Sigma is already gone.
If the Sigma Virus is the true main antagonist then what happened? It seems to be that Commander Sigma tried to fight off the virus. However, the Maverick Virus slowly gained sentience by corrupting Sigma's DNA Soul. In short, Commander Sigma died and there's only Sigma. The Maverick Virus would've started to gain sentience and managed to create a corrupt copy of Sigma - complete with all the original memories while creating a new one. After the original body is destroyed - all traces of the good guy known as Commander Sigma disappeared. In Megaman X, Sigma did announce he would return in the ending and he did for several more games. Destroying Sigma in the first game caused the real deal to be gone and the Sigma Virus to be the new Sigma. Just think of it that the Sigma that they keep fighting against is like a Resident Evil zombie - a reanimated corpse of a dead person. The dead person's soul is no longer the corpse and the real deal isn't at fault for the body's sins.
The dialogue in Megaman X5 would have you question how did Sigma even meet Dr. Wily? If Sigma was really a virus then he could've accessed all the databases of the past. Maybe, Sigma managed to access Dr. Wily's database through Zero and found the blueprints to create what he called was the "ultimate body" as Gamma Sigma. Then again, didn't he have Zero for the time being in Megaman X2 and that Serges could've given him the data? So, it's possible that Serges was a Reploid with Dr. Wily's memories. Another is that the Sigma Virus did also have traces of Dr. Wily's database since it was born out of the Maverick Virus.
Somehow, the more you dig into it, the more you'd actually realize that maybe, just maybe, the Sigma that we kept fighting a malicious computer program. The plot twist in Megaman X4 may have been nothing more than another attempt to add complexity. In total, Commander Sigma no longer exists and all that really exists is the Sigma Virus - an evil version of the noble commander.
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