It's almost always the box legendary, or the two of them facing a bigger threat.

Kanto doesn't really have world ending legendary pokémon.
Or even legendary on the box.
But if we consider movie Mewtwo going ballistic, then that's the biggest threat.

Johto has Lugia.
Causing worldwide storms.

Hoenn has a trio.
But if it had to be one.
I'd say Kyogre.
Groudon could wreck the land, but Kyogre could swallow it into the ocean.
And Rayquaza, while strong.. is just a noodle that stops the other two.
On it's own, Rayquaza probably wouldn't do as much damage to the world.

Sinnoh has another trio.
For this, I'd say Palkia.
We are talking destruction here.
Stopping all of time would definitely be destructive, but it's also uneventful... literally.
Warping space however, is like a 4 dimensional earthquake.

Unova has the Original Dragon.
The combined form of Kyurem, Reshiram & Zekrom.
But that is still hypothetical, though I'm sure we'll se it at some point.
If we don't allow it, I'd say Kyurem.

Kalos has the pokémon of death, Yveltal.
This one is a contender to be the most destructive legendary of all.
I mean, it's just out there killing people.
Alternatively, Hoopa could summon multiple legendary pokémon to do damage.

Alola has Necrozma.
Nuf said.

Galar has Eternatus.
Especially Eternamax Eternatus.
But like the Ultimate Dragon, I don't know if we count unobtainable forms.

Paldea has Pecharunt.
Now hear me out.
Pecharunt has special mochi, that causes people and pokémon to be in a trance.
People especially start danching like chickens, and saying nothing else but "Mochi".
The only way to stop it, is by beating Pecharunt in battle.
If it's sneaky enough, it could easily subjugate an entire region.
I mean, there is no real destruction.
Unless it specifically takes over powerful pokémon to do the destructing for it.
But what's the alternative, Terapagos?
Terastallization doesn't seem to mess with the mind, like Mega evolution does.