A bioweapon spill or war
One of the things that would affect only the planet below and not humans in LEO would be an airbourne virus or plague.
I'm going to take a few liberties with 'Current' technology here, but what I suggest is feasible and essentially boils down to 'incredibly virulent bio weapon'.
As the virus is a weapon, then either it gets out because of an accident or it is used in anger and targeted (in large amounts, all over the globe).
It could be presumed to be natural although for me, this is more of a stretch (ever seen that film with Mark Whalberg where the trees make everyone immediately suicidal? I spent most of it unable to suspend my disbelief).
Obviously it would not be able to leave the atmosphere unless ferried up to the astronauts with a supply shipment somehow, or the group who unleashed it targeted them. So they could be considered safe (or they dodge the missile somehow).
Of course hermetically sealed shelters, submarines, etc would not be affected by this, and there are problems with the timeline - unless you take some creative steps with the nature of the plague.
Drawing some inspiration from the idea of a virus bomb similar to the ones depicted in the warhammer 40k books, it could be engineered to destroy all life and also circumvent normal air filters (by being too small or by being able to dissolve rubber on contact, etc..). Being engineered, it burns itself out quickly and becomes harmless, so the astronauts won't get infected when they land.
If it was virulent enough it could explain why normal gas masks and weakly sealed shelters would fall - but it still leaves stronger stuff like millitary bunkers, submarines etc.
This is where the engineered part comes in - This allows you some scope to explain how hardened installations were overcome, they could have been hit directly with warheads containing the virus.
If the virus were to essentially speed up decomposition, and it was a single event in time rather than spread out, you could also play with the idea of setting the atmosphere on fire due to the huge amounts of released gas - plausibly this might take less than 8 months to burn out but as nobody has ever done it before (thankfully!) it may take more or less time.
Also, if it was transferrable through water aswell as air, it could kill all ocean life aswell as take care of those pesky submariners by infecting the water around the sub, which is then taken in and distilled into fresh water (most subs apparently do this, and also can use it for CO2 scrubbing.) That's your vector to kill off the submarine crews.
What would it be like?
If you burn the atmosphere:
The oceans may have boiled? This would take care of the submarines. Otherwise, you essentially have a blackened and charred wasteland with no surviving organic life and no oxygen left in the air. Pretty hellish.
If you don't burn the atmosphere:
Everything organic is dead and decomposed (at an optionally accelerated rate).
The oceans are filled with decomposed fish guts and other matter, and the atmosphere may have alot of methane in it.
As no world-ending firestorm happened, the infrastructure, technology and buildings are still intact. Also, canned food might be, depending on how virulent the virus is.