For killing a Mega, the starting point is probably this:
Bring down Wal-Mart.
Wal-Mart's income right now is a bit higher than the megacorps in teh first corp guide, and it has teh international scope and scale or a Shadowrun mega. It's in dozens of countries, employs hundreds of thousands if not millions of people, and is diversified into a staggering number of fields, many of which you'd not expect. It tells suppliers how to make their products and what prices that they'll get, and if that drives a supplier out of business, too bad, they can always find another.
So, figure out a way for a team of five Shadowrunners to erase Wal-Mart, and you'll have a start on how to take down a mega. Mind you, the megas have extra-territorality, GOBS of guns, magic, and top-end Matrix support on top of this, so...