In the case of a pandemic, first would be to look at the WHO, And in America you'd look to FEMA to implement the response... So we would go look at their disaster response plans, and those responses are all seem to involve effectively martial law, forced vaccinations and quarantines of entire regions and just allowing those quarantined to die.
Meanwhile the government would find its way into deep underground bunkers, ships in the middle of the ocean, e4b's, etc...
We could argue on the merits of those plans in that particular, but the gist of it is that, if push comes to shove the government has no intention (and probably not enough resources) to take care of you or your family...
My ony point is that we can't be delusional about our importance.
Actually, it would not be the WHO or FEMA, but the CDCP (Center for Disease Control & Prevention) along with USAMRIID (United States Army Medical Research Institute of Infectious Diseases). CDCP would be responsible for detecting the wild nature of a pandemic, and then in cooperation with USAMRIID would then work to actually help control the spread and hopefully contain it.
Because this would be a virus, and other then vaccination and quarantine, there is absolutely nothing we could do. And no, no forced vaccinations, but forced quarantines would be done as a way to contain the disease. But this would be in no way done under FEMA, this would be a military operation.
FEMA's only responsibility would be as it is in any disaster, picking up the pieces after it is all done. FEMA does not go in and rescue people from a disaster, it does not build hospitals to take care of the sick and injured. All it does is try to manage things, generally after everything has gone to hell and somebody else has already picked up the pieces.
And yes, the military is the best and most logical choice for this type of operation. Not only are they trained and have the equipment, but they are also widely inoculated against everything from flu, small pox and anthrax to plague and H1N1 (it seems like every 2-3 months I am getting some new inoculation against something, or a booster for one of my older inoculations). The military already has over a million people with training in protective clothing, decontamination, and managing large-scale facilities of this kind. Nobody else in the country has that kind of training and experience.
And certainly not FEMA, that is not their job.
However, the disposal of the bodies is justifiably part of the FEMA area of responsibility. Because the CDCP, USAMRIID and military are going to be to busy trying to get things under control and taking care of the living. Let FEMA handle the dead.
And no, "the government" will not find it's way into underground bunkers, because that is the absolutely worst place to go in a pandemic. They would simply get inoculations if they have not done so already, and continue doing what they do. And yes, our ships could stay at sea, only if they were there before the outbreak started and are sure that nobody on board is infected. At least until they run out of food.
And if somebody on that ship is infected, they will be returning to port at flank speed. Because absolutely nothing spreads faster on a ship then disease. The tight living quarters, lower sanitation requirements (water is a restricted commodity) and close working conditions means that within a week, generally everybody on board gets sick when a new bug comes on board. I have seen this myself, with an entire Company of Marines to sick to do anything when somebody brought the Flu into our berthing area.