Chronological Order: DMC3 -- DMC1 -- DMC4 -- DMC2
DMC3: Dante and Vergil meet after their meeting a year ago on their birthday. They fight. The End.
DMC1: Vergil and Dante fight (again). Vergil gains his memories back after having them being taken away by Mundus. He explodes. The End.
DMC4: Dante and Nero fight. Dante only recently discovers the existence of his nephew. He's purposely vague, much to Nero's (and the audience's) frustration. However, Nero figures things out for himself, and lets Dante go on his merry way unceremoniously, leaving the fans more confused than ever. The End.
DMC2: Dante is like, super-depressed and dark and brooding. I prefer this version. Dante goes to hell because he has nothing left to live for. Perhaps Nero died. One can only hope. The End.
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According to the "official" timeline, Vergil would've had to have been 11 years old to sire Nero. So, the only way to fix this is to make Dante 39 years old in DMC4 instead of 29 years old (as it's speculated by the fans).
So, in other words, every time Vergil enters the picture, a retcon needs to happen. In DMC1, he was supposed to be dead for 20 years, but it turns out he has only been dead ever since he fell into hell in DMC3 because Mundus "killed" him or whatever.
So, Vergil loses himself to evil, sires a son at 18 years old (he and Dante are 19 in DMC3) and tries to raise his power level in order to protect his son.
In case Vergil failed, he sent his son off to the orphanage. Vergil then fails at the hands of Dante.
He is either now newly resurrected, or has been alive in hell all this time in a "Sleepwalking Mode" and has only just now been able to get out because Mundus was sent back into the Underworld by Dante (allowing for Vergil's escape, seeing as how Mundus' power was now greatly reduced).
Or, Vergil created a "magical clone" of himself at the age of 11, and left it on Fortuna (he gets to Fortuna using a hell gate or something). At the age of 18, he returns to Fortuna, and gives Nero a piece of his soul in case Nero should ever need help.
That "Soul-Piece" then transforms into Nero's arm when Nero was attacked in Mitis forest (right before DMC4 begins).
And the rest is history.