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Ok so I’ve been having some issues with my car. First one of my fans went out. Ordered a new fan assembly. Replaced it. Couldn’t get them to run unless I direct wire them to battery. So they’re now on a toggle switch :( AC stopped working when fans went out. Never got it to work again. Then had a flat tire and being in Texas I about had a heat stroke on the side of the road. So I let my friend drive my car to his house after he put on my spare. He said all he did was remove my speaker from my trunk so no one tried to steal it. When I came to try to fix ac next day car won’t start but when i turn the key all the lights come on and little lock symbol is showing up on the dash. I’ve checked every fuse. Just recently when I turn key on it started doing this flashing of every single light in the car and a loud clicking noise. Me and my cousin tried to follow the clicking noise and at first I thought it was coming from the fuse box near the passenger floor board. I was wrong. My cousin found two more relays near a black box that is under my radio behind a metal plate. What are these relays for? What’s the black box? This car is driving me crazy!!
 

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2011 Malibu LTZ 3.6L V6 Red Jewel Tintcoat
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You haven't found all of the fuses yet, either! Your car has 3 fuse boxes: under the hood next to the battery, under the center console next to and part of the BCM (body control module), and in the trunk on the left side behind a little carpet "door".

All that clicking suggests that the battery has not been charged fully, or something may be discharging it more than it can handle. The terminals could be loose or dirty, or one of the cables could be damaged. Modern cars have pretty much become computers on wheels, and a low battery can cause all sorts of seemingly unrelated issues.

Is the CEL on? If so, have the codes read so you'll have a better understanding of what the has recorded as an issue. It could be related to what's happening.

You mention a speaker in the trunk. If the radio and/or the remainder of the audio system has been modified, the work that was done could be part of the problem as well. Not always, but it pays to look into all the possibilities.
 

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2011 Malibu LTZ 3.6L V6 Red Jewel Tintcoat
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The alternator is controlled by the BCM. In years gone by, there was a regulator built into the alternator, and before that they were a separate device mounted in the engine compartment.

That said, if the alternator is weak, then that could definitely be an issue.

Is the CEL on? (Asked above.) If so, have the codes read, or borrow/buy an affordable code reader and read them yourself. That is the first step in computerized cars.

Unhooking the stereo won't necessarily undo any wiring damage, if there is any, or any short-circuiting that happened when it was installed, again, if there was any. It'll simply remove that load from the battery. If removing it solves your issues, then it's a good idea to review how it was installed and look for any problems that it could have caused.
 
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