The New York Times is reporting that the NSA developed a way to spy on our emails even after the program allowing it to do so was shut down. Until December 2011, the agency was entitled to bulk-collect emails at will because it was subject to oversight from the intelligence court. That meant that the data had to be used according to the regulations laid down by the Foreign Intelligence Surveillance Act. The NSA, however, had a second, more secretive program, based overseas, that did a similar job, but was under no such legal restriction. As such, when its powers were curtailed, it simply went back to doing what it always did, but in a foreign country.
The paper secured this disclosure after going after the agency with a series of freedom of information act requests. The report explains that the NSA wasn't able to read the text of a message, but could identify the "social links" that were revealed by email patterns. The outfit was able to trawl so much domestic data because information is often shifted between servers in different countries. It's this free movement of information that troubled European lawmakers so much that they suspended Safe Harbor between Europe and the US.