One rule: it cannot be caused by aliens or AI invading the planet. But it is okay if an alien race causes the destruction in any other way.

It's an Earth-like planet. I need the effects of the destructive event to be continuous there-after, i.e massive storms and natural disasters for years to come that threaten the small population that survived the initial event in bunkers.

I want the majority surface to get wrecked. I need all things that are required to rebuild a civilization to survive, i.e, an atmosphere, because I need characters to come up from the bunker and be able to live. I don't want them to be comfortable. Their lives are to be miserable. The planet should look like a hell-scape afterwards and they should desire finding a new home.

Hope you don't consider this a duplicate question because I feel my question is more nuanced than any others on this site.

Edit #1

This human race is quite advanced. They'd have technology to redirect asteroids, comets, etc. Unless an alien race were to guide some into the planet.

Edit #2

It's can't be something that effects all planets in the solar system, just the one planet.

/Their lives are to be miserable./

I know a recipe for miserable.

Flies everywhere.

https://en.wikipedia.org/wiki/Black_fly

The flies are a genetic modification attempt gone wrong. They are everywhere and they attack anything that moves, biting and chewing and drinking. They cause blindness and carry other diseases as well. Attempts to control them with pesticides wound up wiping out other aspects of the ecosystem - agriculture crashed and with it, civilization. The bunker was not necessary for the flies, but it was for the fall of civilization and the chaos that followed. The genetic germ weaponry used in some of these wars wound up getting picked up by the flies as well, and now those diseases are also transmitted.

The flies did fine with all that. They are still out there. It is their world now. The humans know they are out there, because somehow now and then one gets into the bunker.

A significant increase in global volcanism would satisfy your requirements:

1. The devastation would be widespread, varied, and continuous. Think of something on par with the formation of the Siberian Traps. Such eruptions can last millennia.




2. The resulting nuclear winter would wreak havoc on the biosphere and agriculture, necessitating greenhouses and artificial light, but the atmosphere would still be breathable over much of the planet within the expected lifetime of a human civilization. Weather nearest the eruption site(s) would be turbulant year-round, and if the eruption is near an ocean the interruption to currents would have chaotic butterfly effects around the globe.




3. The cause could be entirely natural, from an abnormally large mantle plume, for example, or alien-induced (perhaps a microsingularity or other weaponized hypothetical physics).

Due to an edit of the question, this answer has been made invalid. I may post another.

Nearby Supernova.

Dr. Mark Reid, a senior astronomer at the Harvard-Smithsonian Center for Astrophysics stated:

… were a supernova to go off within about 30 light-years of us, that
would lead to major effects on the Earth, possibly mass extinctions.
X-rays and more energetic gamma-rays from the supernova could destroy
the ozone layer that protects us from solar ultraviolet rays. It also
could ionize nitrogen and oxygen in the atmosphere, leading to the
formation of large amounts of smog-like nitrous oxide in the
atmosphere.

Pretty unpleasant, no laughing matter - killing off huge swaths of animal and plant life some would recover in time but not without huge changes, the nitrous oxide would cause serious warming:

On a per-molecule basis, considered over a 100-year-period, nitrous
oxide has 298 times the atmospheric heat-trapping ability of carbon
dioxide (CO 2)

A hot Earth then, but what about the oceans:

....phytoplankton and reef communities would be particularly
affected. Such an event would severely deplete the base of the ocean
food chain.

It's clear that if you take away the base of a food chain then the whole thing falls flat.

Sure, deep ocean life feeding on bacteria at oceanic vents might be ok, but everything else would radically shift.

Given time, technology and resources to shift everything back and make new plantings and reseed the oceans with life - it could be done, but it would be harsh.

A chemical treatment for a global problem gone awry.

Imagine the planet was headed for a man-made disaster - pollution, starvation, disease, etc., and the proposed solution by one of the superpower governments was a chemical release of an antidote high in the air.

There was a second warring nation who wanted to be seen as the savior of the planet. They created a different chemical treatment, but had a similar plan to release theirs into the sky.

The rest of the world was opposed to any global releases of any kind of chemicals, but had no solutions of their own.

Because the governments were at war, cooperation with the enemy was treasonous. Neither side discovered until it was too late that their differing plans and chemistries were incompatible, and when combined produced destructively acidic solutions that eventually broke down into flammable gasses. Acidic fog followed by firestorms swept across all the habitable regions of the planet.

The acid in the air penetrated everywhere, corroding virtually every bit of iron and steel and structurally ruining most buildings, bridges, vehicles, and infrastructure, which then collapsed in the fires. Smoke clouds blotted out the sun, ushering in an ice age in all but a narrow band around the equator. The ash cover killed most remaining plant life. The seas are covered with algae, and few fish species survived. Molds and fungus cover most things. For some reason, some lichens adapted and are one of the few things that still grow.

The clouds have cleared and the atmospheric acid is mostly gone now, so the air is breathable. Fresh water stores can be replenished from rains, but groundwater is not potable. Some lichens and algaes turn out to be edible, but most are toxic. Machinery and vehicles were destroyed by corrosion. Animal life on the surface has been reduced to insects - no vertebrates survived.

Sound hellacious enough for you?

Nukes.

That is actually the plot of every Fallout game ever.

Russia and the US ha e enough nuclear bombs to strike the surfave of the whole world. For the classical atom bomb, with a ground-level burst, the area of impact will be dangwrously radioactive for one to five years. Some time later there will still be radiation, but won't be as dangerous.

If every city and town in the world is nuked, only people in bunkers would survive. They would come out to see nature having taken a manor impact too, as the oceans and rivers will have taken a lot of radiation as well. Every ecossystem would be impacted, even if indirectly. The world will never be the same.