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.