Finding People's Location Based on Their Activities in Cyberspace

Glenn Greenwald is back reporting about the NSA, now with Pierre Omidyar's news organization FirstLook and its introductory publication, The Intercept. Writing with national security reporter Jeremy Scahill, his first article covers how the NSA helps target individuals for assassination by drone.
Leaving aside the extensive political implications of the story, the article and the NSA source documents reveal additional information about how the agency's programs work. From this and other articles, we can now piece together how the NSA tracks individuals in the real world through their actions in cyberspace.
Its techniques to locate someone based on their electronic activities are straightforward, although they require an enormous capability to monitor data networks. One set of techniques involves the cell phone network, and the other the Internet.

Tracking Locations With Cell Towers

Every cell-phone network knows the approximate location of all phones capable of receiving calls. This is necessary to make the system work; if the system doesn't know what cell you're in, it isn't able to route calls to your phone. We already know that the NSA conducts physical surveillance on a massive scale using this technique.
By triangulating location information from different cell phone towers, cell phone providers can geolocate phones more accurately. This is often done to direct emergency services to a particular person, such as someone who has made a 911 call. The NSA can get this data either by network eavesdropping with the cooperation of the carrier, or by intercepting communications between the cell phones and the towers. A previously released a Top Secret NSA document says this: "GSM Cell Towers can be used as a physical-geolocation point in relation to a GSM handset of interest."
This technique becomes even more powerful if you can employ a drone. Greenwald and Scahill write:

The agency also equips drones and other aircraft with devices known as "virtual base-tower transceivers"—creating, in effect, a fake cell phone tower that can force a targeted person's device to lock onto the NSA's receiver without their knowledge.

The drone can do this multiple times as it flies around the area, measuring the signal strength—and inferring distance—each time. Again from the Intercept article:

The NSA geolocation system used by JSOC is known by the code name GILGAMESH. Under the program, a specially constructed device is attached to the drone. As the drone circles, the device locates the SIM card or handset that the military believes is used by the target.

The Top Secret source document associated with the Intercept story says:

As part of the GILGAMESH (PREDATOR-based active geolocation) effort, this team used some advanced mathematics to develop a new geolocation algorithm intended for operational use on unmanned aerial vehicle (UAV) flights.

This is at least part of that advanced mathematics.
None of this works if the target turns his phone off or exchanges SMS cards often with his colleagues, which Greenwald and Scahill write is routine. It won't work in much of Yemen, which isn't on any cell phone network. Because of this, the NSA also tracks people based on their actions on the Internet.

Finding You From Your Web Connection

A surprisingly large number of Internet applications leak location data. Applications on your smart phone can transmit location data from your GPS receiver over the Internet. We already know that the NSA collects this data to determine location. Also, many applications transmit the IP address of the network the computer is connected to. If the NSA has a database of IP addresses and locations, it can use that to locate users.
According to a previously released Top Secret NSA document, that program is code named HAPPYFOOT: "The HAPPYFOOT analytic aggregated leaked location-based service / location-aware application data to infer IP geo-locations."
Another way to get this data is to collect it from the geographical area you're interested in. Greenwald and Scahill talk about exactly this:

In addition to the GILGAMESH system used by JSOC, the CIA uses a similar NSA platform known as SHENANIGANS. The operation—previously undisclosed—utilizes a pod on aircraft that vacuums up massive amounts of data from any wireless routers, computers, smart phones or other electronic devices that are within range.

And again from an NSA document associated with the FirstLook story: "Our mission (VICTORYDANCE) mapped the Wi-Fi fingerprint of nearly every major town in Yemen." In the hacker world, this is known as war-driving, and has even been demonstrated from drones.
Another story from the Snowden documents describes a research effort to locate individuals based on the location of wifi networks they log into.
This is how the NSA can find someone, even when their cell phone is turned off and their SIM card is removed. If they're at an Internet café, and they log into an account that identifies them, the NSA can locate them—because the NSA already knows where that wifi network is.
This also explains the drone assassination of Hassan Guhl, also reported in the Washington Post last October. In the story, Guhl was at an Internet cafe when he read an email from his wife. Although the article doesn't describe how that email was intercepted by the NSA, the NSA was able to use it to determine his location.
There's almost certainly more. NSA surveillance is robust, and they almost certainly have several different ways of identifying individuals on cell phone and Internet connections.
As fascinating as the technology is, the critical policy question—and the one discussed extensively in the FirstLook article—is how reliable all this information is. While much of the NSA's capabilities to locate someone in the real world by their network activity piggy-backs on corporate surveillance capabilities, there's a critical difference: False positives are much more expensive. If Google or Facebook get a physical location wrong, they show someone an ad for a restaurant they're nowhere near. If the NSA gets a physical location wrong, they call a drone strike on innocent people.
As we move to a world where all of us are tracked 24/7, these are the sorts of trade-offs we need to keep in mind.