In EB64 it starts out with something making an odd noise which makes Clint go investigate. Here is what I think happens. Now this is where guessing starts. I think Giygas didn't die. Pokey starts his pig army.
Pokey is the leader of the pig army.
I don't know whether this is a theory on Giygas or Pokey after all this, but it seems right. That game hinted to every game that would soon come out for N64. Pokey is a well built character, he would be a perfect canident to be in Mother 3. I think that Pokey will indeed be in EB64. In EB, my opinion is that Pokey and Giygas were slowly changing places, without Pokey knowing it.