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Not Just a Conspiracy Theory
Simply put, yes, it can be done.
Technical details aside, your cell phone can be remotely powered on and off without either your consent or your knowledge. This includes any tracking functions, such as GPS or just using normal cell tower ping triangulation, and even features like direct microphone feeds for any ongoing conversations (known as a “roving bug.")
Of course, this can't be done for any great length of time, as the cell phone battery will need to be recharged eventually, which puts something of a limit on it.
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Who Does It?
As you might guess, such remote access might take a pretty good hand at hacking. The technical skills required to pull such a thing off are out of the hands of even most programmers.
Cell phone companies, of course, have complete access to your phone and its functions. While the company can't legally just look into your location on a whim, employers do have this power and abuses are always, always possible. A somewhat recent example of some non-tracking abuse is Verizon employees poking into Barack Obama's phone records.
Warrantless cell phone tracking has been a part of the US government as long as there have been cell phones, and cell phone companies are forced by law to hand over any amount of control over these cell phones as either the state or federal government desires. This is for certain once the authorities have a good case for probable cause, and somewhat more borderline if they haven't gone ahead and gotten a proper warrant. This includes location data for tracking purposes. There is a possibility that the FBI does such tracking independently of the phone company, but this is rather difficult to verify.
This doesn't mean they're tracking everyone in the US at all times; only a few Big Brother theorists will make that claim. However, they do have the resources to actively track and analyze many many people at once, and they use this capability frequently for purposes of tracking criminals and suspects.
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As you might imagine, this can constitute a major breach of ethical protocol. Gathering such intimate information as location without either knowledge or consent is a major privacy violation. Particular to the United States is a potential 4th Amendment of the Constitution violation against unreasonable search and seizure.
These techniques are largely used with good intentions. For instance, that “roving bug" concept, remotely turning on the microphone of the cell phone to listen in on conversations, is largely used on suspects who are otherwise impossible to track. Preventing people from violating restraining orders is another potential use, as is tracking suspects such as this brother pair in Italy.
Still, this doesn't sit well with a lot of people. Many feel that abuse of power is just too easy in these situations, and that end does not justify the means when it comes to violations of privacy. This has led to many civil rights organizations leading lawsuits against the government demanding transparency to these tracking practices—and their eventual end.
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Scary. So, how do you avoid being tracked in this manner?
The only real way is to remove the batteries of the cell phone. This renders the cell phone completely useless. However, without power, there is nothing that anyone can do to get any of the functions of the camera up and running.
A few people have gone ahead and created those lead lined bags to keep any signals from entering and leaving the phone, but that's probably a bit of a paranoia stretch for most people.
Of course, neither of these exactly render your cell phone especially useful. The point of a cell phone is to be able to make and receive calls, and you can't do that when the power's off.
So, you're out of luck. Sit back, relax, and hope nobody's watching.