Hi, first time writing a request here.
Have a 2004 4Runner.

A few months back my battery was drained by a faulty radio. Jump started and took it to a shop where they verified the battery was a little bit low but good, they said the alternator was low. I did nothing else, since I understood that if the alternator was not working, I would not have been able to get there, from a 25 minute ride on a jump started auto. No battery warning light at this event.Last week Battery warning went on and off maybe three times, it was during the day. Got home and verified voltage it was over 12 (but not sure how much higher) neither remember if I tested it with the engine running. My bad... Ran during that night and nothing happened. A few days later, driving on heavy rain with lights, A/C, wipers, battery warning again, but this time it did not turned off. Checked voltage and it was low, below 12... had to reach home so continued driving until it died.

Removed and charged battery, just to be able to get home. When battery was connected, alarm goes off, which is a problem for me because maybe a year after I purchased this runner at a Toyota Dealer, the FOB’s stopped working, and every time there a battery issue, the alarm goes off when power is reestablished. I have been disabling through the valet switch, but it also broke a year ago. So this time with just a few on off ignition switch cycles it was silenced and I was able to drive home.Once at home, removed alternator and bench tested at shop. HE said it was good, reading of over 15 V. LEft the battery charging overnight. NExt day I verified all the fuses (except the 140 for fear of breaking it, but it does look ok). Cleaned most of the connections I could identify. Installed the alternator and battery (alarm goes off again but this time the ign on off trick did not worked, so I took what is left of the valet switch and figured a way to do the contact and disabled (silenced) the alarm ). Checked battery voltage with and without engine running, with 12+ and 13+ volts readings. Drive around town for a few minutes and no battery warning light. Returned home, to finish cleaning and later went out again to test with additional power load, and only by turning the headlights, after a few minutes, the battery warning lit again!Returned back home, not very happy. Left battery charging overnight. Next day, after doing some more research, continued looking for bad connections, fuses, etc. Connected the battery and something odd happened. The alarm did not went off! Even so, I did the disabling steps, but noticed more dash lights than normal. Among with the battery, there was ABS and Brake light on. Started engine and measured voltage and now found no voltage increase with the engine running. At some point was going to test ride but then I noticed the shift was locked. Also, windows, wipers, signal light and radio was not working. Forced the transmission to shift into reverse and drove for a few minutes, once forced, shifts as normal, but if put in parking, I do have to force it again.What could all this be? Is this related to the alarm? I tried to locate the module to disconnect, since I have not been using it for almost 13 years, it is only to scare the hell out of me when messing with the battery. Can the alarm block all these items? Is it all related to the charging system issue I have? If it is the alternator, why it tested ok at the shop and then is not working? If the alternator is working, could it be other part of the system? Any ideas will be appreciated.

 

Too tired for a good explanation and diagnosis.

Your battery doesn't take and hold charge, replace it, it's overstressed the alternator, replace it. Your fobs need cleaned and new batteries also probably but your going to have to get the dealership to fix that one unless you can get one to work long enough to reprogram the others to the vehicle.

All the rest is due to low voltage

 

Took the alternator to other shop, it was bad. Replaced it. Not sure if it was initially good and ended killing it during the process, or the shop tech was also tired and did not provided a goon diagnost.

The second issue, power window not working, no signal light, etc. Found a faulty fuse.

Third issue, alarm: once the FOB stopped working, I took it to the dealer. $60 for reprogramming. My response was "you tell me what caused them to unprogram so I can prevent it, cause I will not be here paying $$ everytime they need to be fixed like that. He did not have an answer, so I did not get them fixed. A few years back my wife took it to the dealer again and they tried to reprogram, but they could not. Believe me, I have cleaned and replaced batteries before asking for help.

Next step is to take the battery to be tested. In the two days since I replaced the alt, the voltages has hold.