There have been many predictions as for what occurrence will end the world. Personally, I think the most likely cause will be a breakout of a disease we are not immune to. We know it's very possible. Just take a look at the Swine Flu - it's killed countless people. But what if something sort of like H1N1 broke out again, only this time is was so out-of-this-world that the human body simply couldn't grow immune to it, no vaccine on earth could destroy it, it spread faster than we can act, and alls we can do is sit back and watch it kill off the human race.

As a believer in the Ancient Astronaut Theory, I also think that it is very possible that extraterrestrials will come in 2012. But I believe they would want to make peace with us rather than destroy us - intentionally.

This is my theory - In 2012, ETs will re-enter the realms of Earth, wanting to make peace and conjoin our kinds. With them, the ETs will also unintentionally bring alien diseases and viruses to earth. That means people all over will catch these illnesses and fall into a mass homicide. It could be sort of like the Extraterrestrial Flu.

If the ETs do come, it's pretty likely that they will make themselves seen all across the globe rather than in one place. This means that it will take virtually no time for the disease to spread worldwide.

The worst part about the Extraterrestrial Flu would be that it would be completely unearthly. What is so bad about this is that our bodies are unable to recognize the illness. They said the same for H1N1-an earthly virus. Imagine how many times worse it would be for an unearthly virus.

However, if the ETs are smart, they will wear protective gear that wont allow bacteria to leave there bodies. But they only have so much power over Nature and one way or another somebody will be infected with this alien illness. That person could infect other people, and those people could infect more people, and so on.

In the case of the Swine Flu, we came up with a vaccine so much less people would catch it. In the case of an Extraterrestrial Flu, we only have matter found here on earth to make vaccines for illnesses found here on earth - alien illnesses would call for alien vaccines. Hopefully, the ETs could help us come up with a vaccine using material from their own planet(s). Chances are we will have to wait awhile because they probably wouldn't be used to the disease either because their ET bodies are already immune to this bacteria. The wait could be too long and by the time we see a vaccine it may already be late.

But since they visited before, wouldn't we also be immune due to genetics?

Alot of 'ifs' and speculation in the OP. Aside from my bias opinion that aliens will make an appearance in 2012, I also disagree with the populace being wiped out with an other worldly pandemic.

Think about it, If these alien visitors can travel light years across universes, Is it really beyond them to have a cure for all diseases? I don't think so.

Secondly the swine flu killed roughly 17,000 by the end of 09 which, if compared to other pandemics, is minor. So if the alien virus is as you theorize. I very much doubt that it'll be the end of us... We're more likely to make an exit during a nuclear holocaust started by us.