I'm going to repeat my suggest of a disease/environmental change/something that prevents reproduction. Yes, it's been done, but so has every other idea. Edited to add: If a disease that halts pregnancies months in, it could spread unchecked for that many months. And then it would take the maximum human (or whatever) lifespan to destroy the race. Edited again to add: Of course, this assumes that cloning hasn't been perfected.
Having a comet survive that trip is one big leap of faith, and time. If they're still stuck on their own planet, it should be fairly easy to kill them. Civilization's that have escaped their own cradle are the ones who would be difficult to exterminate. It would just be a twisted 'game' of infinite whack-a-mole. I can give you a few quick suggestions: Technological disaster - an advanced civilization will depend highly on it's tech. A software bug or some technical fallacy could have the potential to wipe them out. Just imagine if all our nuclear power plants had a simultaneous meltdown. This could come from an intentional source or just a grave misfortune. In reality though, a Russian power plant isn't like an American one, and they aren't exactly connected. So you would need to make them depend on some sort of standardized technology. Environmental Changes - this might be something an advanced civilization could handle, unless you made them depend on their environment for their tech. Could be the core of the planet messing about as well. Spatial Phenomena - I don't know how hardcore you want the story, but you could always throw in some pseudo-science detailing a great deal of different star-trek type of events. Time distortion, local space eruption, dark matter explosion, space storm, green-electorfied-plasmatic-bluegoo filtration accident... etcetera... Biological - perhaps they're going through physiological changes detrimental to their own survival, lacking a specific tech to solve it, but still have old versions of themselves? Like others have said, virus is also a possibility. As far as we know, there are no 100% fatal viruses. But that could change any day, and then we wouldn't know about it anymore... Could be an engineered smart-virus that is very patient. Basically, do you want your story to be strict with science or not? If not, you have a trillion possibilities of extinction, your imagination is your limit. If yes, I would say that you need to look over your plan to use a comet as a survival transport. And look at our society, what are our weaknesses? What do you think they will be in one hundred years? What would happen if our communications suddenly stopped working? There's a lot of options for you!
I like the reproduction issue. Sort of like Children of Men. Maybe the advanced race developed something to help them - a new drug, a new form of technology, etc. - and an unintended consequence was that it made all males (or females) sterile.
Does it even really matter? Aren't they all dead now anyway? If nobody knows how it happened that probably won't make any difference to the story.
If I were the last of my kind because my race died out for some reason, it would definitely matter to me. Look at the Ninth and Tenth Doctors from the revived Doctor Who. Their whole character arcs was trying to reconcile that within themselves, they were the last Timelord because their entire race was wiped out in a huge Time War. I would be pretty damnd miserable, to know that we, such an advances race, is on a steady decline with no end in sight. I'm also a fan of the 'reproduction' problem. Maybe something happened and they're just not able to have any more children? In the Mass Effect series, this was the fate of the Krogans because they had all been whalloped by a heavy dosage of 'genophage'.
The supernovea idea is your best bet, and there is a very useful bit of astronomy on your side. We are in what is called the local bubble. A region about 300 light years across where the hydrogen density is about 1/10th of the rest of the galaxy. The postulate is that it is from Geminga. That was 300 thousand years ago so it's a little too soon for the start of life on earth. The thing is you can't shield from a supernovea since much of the energy is neutrino all matter acts transparent, but not completely transparent. You would have to make the shielding larger than that of the diameter of earth. The only trick is to outrun it. Since the energy drops off with the cube of the distance. you can just outrun it given you have a decent head start. if you want a even more original story. Make it so that instead of a comet they use what is known as a bussard ramjet since then there was hydrogen enough to use. Instead of trying to create life from scratch the alien race creates a virus or bacteria that mutates life in order to create sentience to any creature with a similar nervous system (ie. Homosapiens) or you could go with the original story and make it a farther out system as the setting.
An event that seems plausible but kind of ridiculous could be useful for this race. Imagine life spans that stretch for eons. The people become bored of living such lavish, long lives, and simply stop reproducing, feeling that boredom is a curse. Many countries have very low reproduction levels, though this may not be the reason, so populations can shrink over time.
An inferior, violent and brutal sub-race destroy their superiors. I refer you to History for examples, such as the Roman Empire.
I think as a species we are already sleepwalking into disaster. I think a combination of 'I'm alright, Jack' and 'it'll never happen,' and general disbelief in things that are already happening to all of us (like climate change) will be our downfall. The fabric of our lives in the developed world is already so bound up in communication technology that if it were to suddenly fail ...for whatever reason ...things would very quickly fall apart. How many of us grow our own food? I don't mean have a garden, I mean are entirely self-sustaining? Over the long haul? Can we produce seed for next year's crop? How many of us have access to a woodlot to keep ourselves warm over a period of years ...provided we also still possess wood-burning equipment? How many of us are dependent on certain medications? The more we digitalise our knowledge, the more vulnerable we are to losing it in one fell swoop, if the technology that stores and distributes it fails. If things like utility companies collapse, or medical supplies become unavailable over a wide scale, or we are suddenly unable to move about due to lack of fuel ...or our banking, grocery and other supply systems go down because of a worldwide fault in the technology that keeps them running? It wouldn't take long for civilisation as we know it to disappear, would it? I don't think you need to look too far from home to figure out how a civilisation can suddenly break down.
I think I should point out that this is very similar indeed to the plot of the 1950s BBC TV series and subsequent Hammer film Quatermass And The Pit. The Martians, a race of locust-like hive insects, realize that their world is dying. Lacking the means to travel to another star, the only habitable planet within reach is Earth, but the conditions there, especially the high gravity, mean that they cannot colonize the planet, so instead, they artificially boost the intelligence of the subhuman apes that are currently the smartest creatures on Earth, and attempt to indoctrinate them with their own mentality so that their racial legacy will survive. They are only partially successful, dying out before they can complete their plan. The drama in the story arises from the discovery of a million-year-old Martian spacecraft buried beneath London, the realization that the numerous terrible wars in human history are due to the fact that humans are half-programmed to behave like Martian hive insects with no individual personality and an instinct to ruthlessly destroy individuals who in any way deviate from the norm, and the accidental reactivation of the ship, causing most of the population of London to start behaving like soldier ants.
Isn't there two versions of that? There is a movie "Five Million Years to Earth" and also your series?
I have often wondered about this question in the context of humanity itself. With 7 billion people on the planet, it seems inconceivable that there is not one group of male and female people who could adapt to a post-apocalyptic world. It seems like the entire earth would have to become uninhabitable, e.g. disappearance of the magnetosphere, in order to leave people with absolutely no way to adapt. Even in a crazy scenario like the sun being blocked out, I bet people could still use geothermal energy to derive enough heat and light to survive and grow food. Remember, there are 7 billion of them -- what are the odds that not a single one of them would know how to do this?
This works with everything but the gamma ray burst, which would irradiate every living creature on earth with a lethal dose of gamma radiation in a matter of seconds.
Years ago there was a (sadly) short-lived miniature tabletop wargame called AT-43. One of the factions, the Therians, were the post-singularity descendents of mankind: after eons spent in crafting technological marvels and genocidal campaings in the Milky Way they decided to prevent the Big Crunch of the universe re-engineering the universe, one galaxy at a time. A task that they're doing since time immemorial. With re-engineered bodies, completely different from modern humans, functionally immortal and with a culture that does not have any resemblance with current ones the Therian are utterly alien, even if they're human. The strange thing? They seed habitable planets with baseline human DNA, watching those worlds create cultures and nations...waiting until their industrialization/technology arrives at near-modern level. Then they attack them, dyson-sphere their solar system, and continue their unvierse rearranging plan. For fun. Your technological advanced race could hit a technological singularity, becoming something utterly different and monstrous to the eyes of baseline members of that race. Those "old fashioned" members of the race could send their heritage far away, trying to flee what they perceive as the end of their species. Or what is actually the end of it. The enemy of this race, basically, it's the new iteration of the race itself.
Complacency. Have you ever read The Machine Stops? It's a great story. The humans live in a utopian world made possible by their highly advanced technology. There's no war, no disease, no unhappiness of any kind. Then, the technology breaks. Because they were used to having it so easy for generations, no one knew how to do anything for themselves anymore. They didn't even know how to fix it. A race like that would probably go extinct in a few weeks.
A computer virus that disables all networks and machinery. This could bode fatal if they've evolved technologically to the point of devolving, such as the human race in Wall-E.
