...And that’s why Vergil has been imprisoned on Fortuna all along.
Okay, this is my own headcanon about what happened between DMC1 and DMC5, but it’s actually supportable.
No, really, hear me out. (I’ve even included pictures. At least look at the pretty pictures!)
Approximately sixteen years pass between DMC1 and DMC5. There’s some debate about the exact passage of time, but general consensus based on the books, etc. is that Dante is 28 in DMC1 and 44-45 in DMC5. That’s a long time for Vergil to just be… not around. So where did he go for all that time?
Let’s start with the prequel: At the end of DMC3, Vergil yeets himself off a waterfall into the underworld, and goes directly to challenge Mundus without passing Go or collecting $200 (because that’s a smart thing to do when you’re seriously injured after five consecutive boss fights).
We’ve known all along he was destined to lose that battle. In Visions of V, we see more of what happened: Mundus breaks the Yamato, uses Vergil as a pincushion, and more or less wipes out his sense of self, turning him into Nelo [sic] Angelo. Keep in mind that this name is a known mistransliteration of Nero Angelo, which is Italian for Black Angel. (This will be relevant shortly.)
[Side note: It was pretty darn obvious that Nero was connected to Vergil as soon as they announced the character’s name in early DMC4 promotion, because Nero/Nero Angelo. I mean. They didn’t even try.]
In DMC1, Dante fights and defeats Nelo Angelo, who is last seen surrounded by lightning and glowing, after which his half of the amulet falls to the floor. When Dante looks up, Nelo Angelo is gone. We don’t actually see what happens to him at this point; Mundus just says in the following scene that Vergil has been defeated. Dante assumes he’s dead, but we never see a body.
It’s logical to assume that like Mundus, Vergil gets sucked back into the underworld when everything on Mallet Island collapses. Presumably the shards of the Yamato are still down there somewhere, as well. (Maybe Vergil even collects them. He is rather attached to that sword.)
Meanwhile (and continuing for some years up to DMC4) on Fortuna, the Order Needs More Power™ and is trying to open portals to the underworld to acquire it. They succeed in doing so, somehow recovering the pieces of the Yamato, which they use to force open more portals.
It’s my theory that the Yamato isn’t all they recover – they also find Nelo Angelo, or what’s left of him. They don’t know that he’s Vergil (it’s unclear from the Order’s reaction to Dante whether they’re even aware that Vergil exists), but they do know he’s a powerful demonic creature that they can harvest tissue samples from.
There’s clear evidence for this in the game: On Fortuna, Nero and Dante face numerous enemies who seem to be variations on Nelo Angelo. Most notable is the Bianco Angelo (White Angel), which is said to have been “made from a fragment of a demon known as the ‘dark angel’.”
You don’t have to speak Italian to make the leap from Dark Angel to Nero Angelo, especially since this was translated from Japanese without consideration for the fact that the words were originally in two separate languages. (There are numerous such translation difficulties in this series; see also the reference to the sword names in DMC5, which can only be understood if you know which kanji are used to write Yamato in Japanese.)
Agnus is engineering demon hybrids in his creepy basement lab, which you can explore in Mission 6. In the “Angel Creation” lab there are, among other things, parts of demons or Angelos-in-progress (the gold wing-shaped things) and human bodies in cages. Examining them reveals (via text box) that they are basically soulless shells, presumably having had their souls sucked out to power the Bianco Angelo soldiers. This confirms that Agnus keeps both people and demons in storage for his experiments.
So the rest of DMC4 happens, Dante and Nero take down the Order, the Savior is destroyed, the castle collapses, lots of people die, and whoever is left in charge of Fortuna spreads a cover story that the city was damaged by an earthquake. Since Dante has killed Agnus and most of the Order’s leadership, and it’s stated in game dialogue that very few people even know Agnus or his lab existed, I’m guessing all those bodies hanging around in cages just remain where they are (deep underground, sealed off from the outside) during the subsequent reconstruction of the city. If Nero Angelo is there, he’s staying put for a while.
Five years pass. Nero and Kyrie stay on Fortuna and rebuild. Kyrie runs the orphanage, while Nero opens the Devil May Cry mobile outfit with Nico (per both Before the Nightmare and the DMC5 files).
During this time, Vergil somehow regains enough of his strength to stagger out of wherever he’s been stored/hiding/trapped. His body is breaking down, but seeking the Yamato, he makes it as far as Nero’s garage, wearing a leather cloak strangely reminiscent of the one he wore when he visited Fortuna previously. Maybe he had it stashed somewhere, or just knew where to find another one like it.
So let’s recap: Prior to taking Nero’s arm, Vergil doesn’t have the Yamato, so he can’t open portals. He can barely walk, so he’s not in any condition to travel long distances. He’s too weak to transform to DT, and presumably doesn’t yet have SDT, so he can’t fly to an island under his own power.
He has to already be on Fortuna to be able to get to Nero. And the only way he could reasonably be on Fortuna is if someone – most likely working for the Order – opened a portal and let him out of the underworld, where he was trapped after DMC1. The Order clearly used him to make the Bianco Angelo, and likely kept him contained, since he never claimed the Yamato for himself while it was in the possession of the Order, and didn’t come after it for five years after the Order’s collapse. Evidently it took him that long to get free.
So anyway, there’s my theory about Vergil being on that island THE WHOLE TIME during the events of DMC2, the DMC anime, and DMC4, and Dante never realized he was within arm’s reach of his brother.