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Both groups of Links find themselves in another Hyrule- the same Hyrule. (Wild’s Hyrule, because it’s very unoccupied and open.)
But they don’t happen upon each other.
Instead, they each wander. The DL group is trying to find some sign of current civilization, so they’re aimlessly wandering and making sure Realm doesn’t fall behind and lose himself. Then the Link at the front, Lore, finds a harmless red laser aimed at his chest. He looks for the source of said laser and finds it to be an enormous, creepy machine that reeks of danger.
The lone Guardian attacks, exploding the group apart, and then two more appear, drawn by the ruckus. In the ensuing chaos, the Links enter Survival Mode and it’s all they can do to run out of laser range... before they discover they’ve all scattered out of earshot and eyesight. Wind, unfortunately, has found himself completely alone.
Meanwhile in the Linked Universe group, they’re following a set, specific path to a stable, so they can collect horses for more efficient travel. Unfortunately along the way, a well-timed (or poorly-timed) boulder falls towards the group, breaking it in half, and then an unexpected flying Guardian chases them apart before they can gather their long-range weapons- Wind realizes he ran a little too far, but heading back to where the group was, he finds no one.
Both Winds attempt to find their group.. and almost do.
Dusk finds Wind, and calls out to him. Wind wonders to himself if the Guardian explosions burned off Twilight’s wolf fur, but doesn’t think much of it and groups up with him. Hopefully they’ll find the rest of the guys soon.
Wind, meanwhile, is trying to find anyone- he’ll take Realm, at this point. The misdirectional field might even lead them both directly to the other Links. Then, fortunately, he finds ‘Dusk’.
Through sheer force of story convenience, Wind doesn’t call for Dusk by name, and so he and Twilight pair up to try to find their own groups.
The Dusk and Linked Universe Wind duo find the Linked Universe group. Dusk, upon realizing that these are the wrong Links, lets out a resigned sigh. There’s going to be a lot of story swapping, and given that this Wind is clearly not the Wind that Dusk knows, there’s going to be far more confusion and name logistics before they can get both groups to work together.
Twilight, on the other hand, is fully unprepared to deal with Lore, who immediately deduces that Twilight is not Dusk because he’s not wearing a hat. This ends up being correct, and now there’s a Link missing and apparently nine others out there also protecting the universe. And one of them is a clone of Dusk.