Honestly, given how since Gen 6 the Mythicals have no events or lore that can be adapted into a story, it's kind of hard to think how they could be used. But I'll try.
Here's the thing: There are exactly two Mythical Pokémon that have an exclusive Z-Move. They are Mew and Marshadow. One is pink, a variant of red, and the other is dark green in one of its forms.
When they eventually split USUM into a separate chapter from SM (and they will. Trust me, that finale has a ton of Rainbow Rocket flags, and no third game since Gen 3 hasn't had its arc being separate from the rest), they'll probably have Red and Green partner with them to use Z-Moves. Perhaps they can be hiding in the Battle Tree or something and are found by Red and Green.
Magearna is an artificial Steel/Fairy Pokémon, and thus might be owned by Gladio or Lillie. Maybe it'll be found and revived by Molaine, but I think it'll join either Gladio or Lillie. Maybe it'll go to if they want to reference the anime and keep the stuff from the games where she becomes a Fairy type Trainer. But it might also go to Gladio due to his implied affinity to artificial Pokémon... which they have done nothing with since the tournament in Melemele.
Zeraora is the easiest. First, look at Achroma's hair: He's blond with a blue streak. So is Zeraora. And on top of that, its signature move is named Plasma Fists. Seriously, it's almost like this Pokémon was designed with him in mind. Achroma might capture Zeraora and use it to help fight Rainbow Rocket, or at least the G-Cis/Plasma side of it.
And Meltan/Melmetal. Well, I actually think it might be the McGuffin of the LGPE arc. Everyone for some reason is acting like LGPE is not going to happen, but even Yamamoto, days before the SwSh chapter release, said LGPE has not been ruled out. I'm pretty sure it's going to happen, they just don't have anywhere to publish it yet. Maybe it's even going to be the new B2W2 if push comes to shove. I honestly believe Meltan and Melmetal are more likely to be the main focus in an LGPE arc. Sure, there's a Gigantamax Melmetal, but that doesn't neccessarily mean it's going to be in SwSh. It could be in the DP remake arc if we get DP remakes this Generation, like how some Megas introduced in XY only showed up in the ORAS arc, or heck, maybe in a Let's Go, Phanpy!/Snubbull! arc if they decide to have another Let's Go! game.
However, if LGPE happens, and Kusaka decides to give Magearna to Lillie, maybe it could also show up in the LGPE arc, as both Meltan and Magearna are Steel-type Mythicals. I mean, Lillie is going to Kanto, right? While that is something that happens in the games, I kinda feel like that's also a setup for her to be in the LGPE arc. So, maybe Team Rocket (or GO Rocket) is looking for Meltan, and uses Magearna as bait to attract them, since they eat metal. Or something.
EDIT: Fixed typos.
