I installed an aftermarket stereo system in April of 2007. About August of that year I started to get this whining from the alternator. It seemed at first to only whine in wet weather or when it got wet from an undercarriage wash, but then it just keep whining and seemed to do it more on hot days. New belt, electrical system OK, whine was still there. More than one mechanic said it was from inside the alternator and I'd just have to deal with it or replace it. I dealt with it, then finally, about 3 months ago, the original factory battery went dead and I jumped it and headed to the parts store and installed a new one. The whine magically disappeared, for good. I even drove through the car wash with the undercarriage wash and no noise. Two days ago a deer ran out in front of me and I slammed on my brakes and my subbox with the two amps connected to it got knocked around my truck and my remote amp wires were pulled out and many others were loosened, so I decided to redo all the connections. I of course disconnected the - of the battery and redid everything exactly as it was before. I started my car and the stereo came alive and I redid all my sound settings, I went for a short drive after and thought I heard some radio noise like when someone puts speaker and power wires together and you get that rpm sound when you accelerate. I turned off the stereo and the whine was back! The same exact alternator noise as before. Anyone know what this is about? I'm guessing because I unhooked the negative to work on my system, it reset stuff or something electrical happened and triggered the alternator. I just don't know. Tomorrow I plan to disconnect and reconnect the negative again to see what that does. It just seems that the battery has something to do with this alternator noise. I put in a new one, the noise is gone, I disconnect it to work on my stereo, the noise is back. Any help would be appreciated.

Check the output at the alternator and at the battery. I've heard alternators whine when they meet their peak output or are, in your first instance; connected to a battery with a dead cell. Is it possible you damage the battery in your hard stop?

Sorry. 1999 Bonneville SLE 3.8 3800 Series II

How do I check the output on both, a regular voltage meter? Battery is very new and it wasn't damaged in anyway during my sudden stop. The thing about an alternator whining at max output, would it still whine when the stereo system is off, or are you saying an alternator can be at max output just because the battery could be bad? I'll reply tomorrow after I disconnect the battery again and recheck all my wire connects. Thanks

After disconnecting the battery again, and redoing the 2 gauge that runs from my positive terminal to a 200A fuse, then back to a distribution box that splits it into two 4 gauge that runs to both amps, the noise is gone, for now at least. After the second battery disconnect and a few ignition start and stops, it seems to have reset some things or something. Now when I throw my Bonne out of P-Park I can hear the doors locks automatically lock, it never did this before. And the tiny lights under on the inside door handle now light up, they've never worked before either. HMM Kinda reminds me when I had a 89 Olds Cierra in 95 with a 2.8, I disconnected the battery to install a stereo system and when I hooked it back up the Olds would want to die whenever I slowed to a stop, I'd have to rev it at lights to keep it from stalling, and this was a car that was meticulously taken care of . After about a half dozen ignition start and stops it fixed itself and it ran great for the next 4 years. wtf? It'* the Bonne'* original alternator so I'm guessing I will eventually need to get a high-output one that can handle all the wattage my stereo needs. Thanks for the help.