I'm going for the theory that a shard of Vergil's spirit lies dormant within the Yamato, and when Nero obtains it, Vergil beings to once again awaken, obtaining the Yamato seems to draw out a dormant something within Nero, hell, even his Devil Trigger has the spirit of Vergil's behind him.
Nero uses a LOT of Vergil's battle quotes when executing attacks...And something about Nero mentioning the voice echoing in his mind, "Power...Give me more power!" just gives a rather large hint of Vergil there, I honestly think that something of Vergil is left within the Yamato, just waiting...