The New York Times' first fruits from its collaboration with the Edward Snowden archive shows us how the National Security Agency figures out whether people who associate with terrorists are part of a plot or conspiracy.
Significance: This is the "how" of "contact chaining." Our apocryphal terrorist bad guy in Yemen calls my number, 310-555-3939 in California. The NSA and the FBI then use the database of phone records to see who I've called recently, and who the people that I've called have called. If the numbers match those on a watch list, then the FBI will open an investigation. This article tells us what happens to the OTHER numbers that the NSA has run through its system.
Key point: The NSA can utilize its contact chaining database and perform subsequent analysis on phone numbers "directly or indirectly" connected to a foreign intelligence purpose. Counter-terrorism is one. There are others, like counter-proliferation, counter-narcotics and counter-espionage.
Explanation: The point of having the American telephone number database is to figure out whether people unknown to the government are communicating through intermediates with terrorists. In other to do that, the NSA matches the phone numbers against all of the information it has access to, which consists of the digital network information and content they've legally collected under the FISA law as well as public sources, like Google, or Lexus-Nexis, or Facebook. It "enriches" the number.
I've explained how this process (likely) worked before, not having access to the documents that Snowden provided other journalists. The Times story confirms what one would assume the NSA would have to do with the data it collects in order to assess it for relevance.
What we still don't know: The scope of the domestic email metadata that is obtained through proprietary and legal authorities, and not simply by searching Google.
Harm to national security from publication: None. In my opinion, which is of limited relevance, this article does not damage U.S. national security interests.