Organizations with extensive hacking resources can, and probably do, clone phones. But the ability to clone one phone via another quickly and wirelessly is not possible as it is depicted in Person of Interest.
Tracking people in real time
Phone apps, such as SpyBubble, Mobile Spy, FlexiSpy, StealthGenie and others work invisibly in the background and handle several types of espionage, including real-time location tracking. After the software is installed on an individual's phone, you can watch on a map as he roams around town.
But these apps need to be physically installed on a phone. To the best of my knowledge, they can't be installed remotely, though it's possible that the user could be tricked into installing software with similar functions. This could be done by spoofing a legitimate app, for example.
However, a spy organization or government agency wouldn't need to install an app on your phone to track your location. They only need to gain access to the location tracking that your wireless carriers already do.
Carriers already collect this data and sell it to anyone with the money to buy it. And they routinely provide location data to law enforcement agencies that request it.
Listening through phone microphones
In Person of Interest, the stars use other people's phones as remote microphones for listening in on conversations -- not just while they're on calls, but even when they're not using their phones.
That form of eavesdropping, like phone cloning, used to be a lot easier. Nowadays, I know of no viable generally available software tools that make it possible to listen through a phone's microphone when it's not being used for a call.
That said, all of the standard mobile phone spy tools listed above claim that they offer the ability to listen in on calls as they're taking place.
Reading text messages remotely
SpyBubble, Mobile Spy and other tools also let you grab text messages, both incoming and outgoing. The messages can also be made available to law enforcement agencies by carriers -- and, presumably, they'd also be available to any hacker who can access the carriers' databases.
Apps like SpyBubble and Mobile Spy also deliver a large number of data types from victims' smartphones, including complete call and SMS logs, all contacts, all email, all URLs visited on a browser (including search queries, which are displayed in URLs), all photos and videos taken with phones, and more.
If cheesy apps like those can do it, you can be sure that sophisticated hackers, spy agencies, organized crime groups and others can do it, too.
Bluejacking is the use of Bluetooth wireless technology to either send messages or files to a phone, or connect to it in other ways. The benefit of Bluejacking is that the connection isn't conveyed through a carrier, so it's harder to track. And it's anonymous.
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