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).
astronaut safety
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).
survivors
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.
still survivors?
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.
@jammypeach This is late, but the film you are probably thinking of is "DEFCON 4" (http://www.imdb.com/title/tt0087130/) A fav of mine from the 80's as well :) Also, to the OP, Neal Stephenson's recent book "Seveneves" is an EXTREMELY deep dive into basically this premise.
– Jason K – 2016-07-15T17:22:50.2271How long can the astronauts survive in space while waiting for the planet to be accessible again? Is this something you wish to specify or something the answers should calculate? – trichoplax – 2014-10-15T12:32:05.317
18I don't think a population of 3 is enough to restart humanity. – ratchet freak – 2014-10-15T12:33:57.037
4
@githubphagocyte judging form how often they send food up there (every 2-4 months and their 45-day food reserve which they have almost needed to start digging into, I'd say 8 months is a reasonable, optimistic guess.
– overactor – 2014-10-15T12:40:45.2002If there were a number of different space stations with humans on board, all equipt with a means of falling out of orbit without burning up, and a means of surviving impact, then there could be a larger population that might be more realistic. – trichoplax – 2014-10-15T12:40:52.793
1@ratchetfreak Well, maybe. It depends on who is what gender and how fertile each person is. – Ethan Bierlein – 2014-10-15T12:44:17.857
1@EthanBierlein I can't remember where I saw it, so I can't provide a link (I will edit my comment if I can find it), but I remember reading an article where some scientists worked out that the minimum number of humans you'd need to restart society, with enough genetic diversity to have a decent chance at survival, was somewhere in the 150-200 range. – Nicholas – 2014-10-15T13:47:32.073
6This is essentially the plot of the Bond film Moonraker: Drax builds a space station and plots to conquer earth from it with biological weapons. – pjc50 – 2014-10-15T16:15:08.153
this is also the premise of another american film from the 70s or 80s I think, in which 3 astronauts are stuck in orbit while a war consumes the earth. When they finally re-enter, close to a year after the fact, they find a fallout 3 style wasteland and a society run by a dead general's petulant son and the remnants of a military base. I forget the name though... – jammypeach – 2014-10-16T13:12:44.360
one thing that would achieve what you're looking for however, see the lifeater virus bomb from the warhammer 40k books... it essentially dissolves all biological life above single cell organisms, then burns itself out. The resulting huge amounts of methane produced by the decomposition can then be ignited and essentially burn the atmosphere. that may be over in <8 months, give or take. EDIT - could be considered near-current technology given man-made bio weapons, although very much exaggerated and over-the-top. – jammypeach – 2014-10-16T13:16:17.450
@jammypeach sounds like the beginnings of an answer. – overactor – 2014-10-16T13:17:37.907
I can't edit my comment anymore, but I wanted to add this link: http://genetics.thetech.org/ask/ask113. It is not the one I was thinking of when I wrote my comment, but it contains similar information that supports my point.
– Nicholas – 2014-10-16T18:51:09.333This is more or less the plot of the movie Oblivion.
– Nit – 2014-10-16T19:01:16.567Then there is the The Coming of the Great White Handkerchief but I don't think it will help the astronauts
– MickyD – 2014-10-17T11:01:38.363@Nit I'd disagree with you, having watched that film - but I don't want to post any spoilers so suffice it to say that there are differences. – jammypeach – 2014-10-17T16:18:27.533
1@Nicholas nowadays, the genetic diversity might be "decoupled" from the number of individuals. A tiny population that has an access to frozen contents of a pre-cataclysm sperm bank might avoid the genetic diversity problems. – Peteris – 2014-10-18T13:01:16.233
@Peteris Very interesting concept. But it seems like most of the suggestions below would knock out sperm banks either directly (asteroid) or indirectly (death of all humans stops power generation). So I think the survivors would have needed to plan ahead for your strategy to be viable. – Nicholas – 2014-10-19T19:24:20.837
2@pjc50 Also the entire premise of the recent show 'The 100' - though in this case looking at the 'time to go back' instead of someone trying to make it happen in the first place – Baldrickk – 2014-10-20T09:45:28.143
http://worldbuilding.stackexchange.com/questions/26364/no-newborns-on-earth-how-much-time-to-find-a-cure/26481#26481 – Joshua – 2016-02-08T23:59:32.123