Global Lake Nyos event.
A pocket of magma lies beneath the lake and leaks carbon dioxide (CO2)
into the water, changing it into carbonic acid. Nyos is one of only
three known exploding lakes to be saturated with carbon dioxide in
this way, the others being Lake Monoun, also in Cameroon, and Lake
Kivu in Democratic Republic of Congo.
In 1986, possibly as the result of a landslide, Lake Nyos suddenly
emitted a large cloud of CO2, which suffocated 1,746 people and
3,500 livestock in nearby towns and villages. Though not
completely unprecedented, it was the first known large-scale
asphyxiation caused by a natural event.
The premise for your event: it turns out the climate change deniers were right. Rising CO2 was not man made but due to a gradual, colossal outgassing of CO2 at one site at the bottom of the ocean. Like Lake Nyos, immense amounts of CO2 accumulate. When the meteor hits that area, the water outgasses and a Nyos-like "cloud of doom" rolls over the earth. Animals suffocate. Plants chortle merrily, replete in delicious CO2 and loads of nitrogenous fertilizer. Not only do they survive, they thrive.
Some humans make use of tunnels and other CO2 free air to survive and ride out the trouble.
I am struggling some to figure out how to make this last years. The Lake Nyos event lasted a couple of hours tops. CO2 can definitely kill you and you could throw in a fair proportion of CO which kills you better. But a continued outgassing from some secret source so as to keep the surface uninhabitable strains my credulity.
You could have the CO2 arrive from space - a giant frozen dry ice meteor. A lot. Most of it would sublimate away on entering the atmosphere, creating the "cloud of doom" - a really big meteor but not a really big impact. The rest would turn to gas from the heat of the impact. You could have enough CO2 arrive that it would take a long time to disperse.
CO2 is also good because it is not cyanide or something immediately deadly. It is more interesting and offers more story opportunities to have the atmosphere be bad but not outright lethal - people who had to venture outside would feel sick and hyperventilate as their CO2 level rose and pH fell. The plants would not just survive - many would thrive. Also, there is plenty written about what other things would happen with high CO2 - icecaps melt, poison ivy takes over etc. All of that stuff would happen in fast forward. Humans would emerge into a green, hot, wet, itchy world.