Here’s an article on the subject of cross-nation jurisdiction for Internet activity.
The indictment makes these points repeatedly. Megaupload wasn’t just some Hong Kong enterprise that “happened” to be used by US residents. The site had leased more than 1,000 servers in North America alone; 525 were at Carpathia Hosting and were located in Virginia. Between 2007 and 2010, Carpathia received $13 million from Megaupload. (Cogent Communications in the US supplied a few additional US servers and bandwidth.)