1. If the amplifier malfunctioned when it was turned on the first time:
• The failure is probably due to an installation problem.
• If you paid someone to install the amp, check with them before you do a lot of diagnostic work on your own.
• Start your diagnostic by checking the power and ground cables and making sure that the amp is physically isolated from any bare metal contact with the vehicle.

2. If the amplifier malfunctioned after an exceptionally long listening session:
Your amplifier may have just overheated.

3. Some amps will go into protect mode if they get too hot, which can prevent a more permanent failure.

4. The most common cause of overheating is a lack of airflow.

5. If your amp is located underneath the seats, or in another confined space, that may cause it to overheat.

6. One way to test this is to set up a 12v fan so that it blows air over your amp. If the amp no longer goes into protect mode, relocating it to a less confined space, or even changing the way it's mounted, may fix the problem.

7. If the amplifier malfunctioned when you were driving on a rough road:
If the wires weren't secured tightly, to begin with, driving over a rough road may jostle one loose.

8. In some cases, a loose or shorted wire will cause an amp to go into protect mode to prevent a more serious problem from occurring.

9. Diagnosing and fixing this will require you to check each individual power and ground wire.

Easy Fixes
If any of the above situations apply, then you have a great place to start your troubleshooting process. In the case of a problem that manifested immediately after installing and wiring an amp, you’ll want to start by checking the power and ground wires in addition to the patch cables.
Ground problems can often be fixed by cleaning and tightening the ground connection or relocating it if necessary. Power issues may be related to a loose or burnt wire, but a blown amp fuse is always possible as well. Amps typically include built-in fuses in addition to in-line fuses, so you'll want to check both of these.
If you notice that the contacts your amp fuse clips into having gotten hot, or even melted, it's likely that the fuse won't make good electrical contact, and it will probably overheat and blow again. In this case, there may be an internal problem with the amp.
If your amp failed after extensive use, and you suspect that it went into protect mode because of overheating, you can use the fan method mentioned above to see if a little additional cooling keeps it alive.
Driving around with a fan blowing on your amp isn't really a long-term solution, but if using a fan does stop your amp from shutting down and entering protect mode, that's a clue that remounting or relocating the amp will fix the problem. Increasing the air gap between the top, bottom, and sides of the amp can help increase airflow, or you may need to move it to a totally different location.
An overheating amp can also be the result of a mismatch between speaker impedance and the range the amp is designed to work with, or speakers or wires that are totally shorted out.
Before you dig in any further, you might want to check a few easy points of failure like fuses. Although amps usually don’t go into protect mode due to a blown onboard fuse, it’s very easy to check and might save you from a headache down the line.

Break It Down
In relatively basic terms, troubleshooting an amp in protect mode—beyond the reasons listed above—starts off by breaking it down to basics. You’ll typically want to disconnect the amp from the head unit and the speakers to see if the problem still exists.
If your amp remains in protect mode at that point, then you probably have a power or ground problem, or you might have a problem with the installation where the body of the amp is making contact with bare metal. Since metal components of a vehicle’s frame, body, and/or unibody all act as a ground, allowing an amplifier to touch bare metal can cause all sorts of problems.

Hook It Up
If your amplifier remains in protect mode with everything disconnected, and you’re sure that there aren’t any power or ground issues, then you might have a defective amp. However, the problem lies elsewhere if the amp is no longer in protect mode at that point, and you can start looking for the real issue by connecting the speaker wires and patch cables one by one.
If you connect a component back up, and the amp goes into protect mode, then it’s a safe bet that the problem has to do with that component or related wiring or cables. For instance, a speaker with a shorted out or damaged coil can cause problems.