I have a 2012 Fusion SE. A couple months ago my house was struck by lightning. It did not directly hit my car but the strike did somehow take out the alternator. The altenator was replaced. The battery light stays on. I can't figure it out. Neither can my mechanic. The alt is putting out 14.2. The battery is around 12.8. The car runs fine. If I leave the car off for more than 4 hours, the battery is dead. There is a draw somewhere. What I normally have been doing is simply pulling the positive cable off and reconnecting when I need the car. It does solve the drain issue but when I forget, I have to have the battery recharged, it's too drained to use a jump pack. Another weird thing is that when I'm driving the battery light will go off for a bit every 10 min or so. I had one mechanic say the brown diodes in the engine fuse box were bad. They were replaced and still no resolution. I don't know where to begin.

 

If you didn't get the replacement alt from Ford, suggest you consider putting a Ford reman alt on. You could have more than one problem, but There is a problem with the alt.

 

Was replaced at dealership. Over $650! But I picked it up after service was closed. Took back the next day. Ford says alt and battery are fine. They would need to do more diag to find issue but currently I'm on a tight budget and can't afford it.

 

If they said it was corrected and charged what they did, they need to make good on that repair that didn't correct the problem.

 

There are at least 2 ways to attack a problem like this.
One is to watch the battery current with everything off and vehicle parked for at least a half hour to allow time for modules to get into sleep mode. Then pull fuses to watch which one causes the current to drop when the fuse is removed. It is not the best way to go after the problem, but may help direct the checking to a particular system.
The better way is to use the voltage drop system with everything off doors closed and check for voltage drop across each fuse . After the sleep mode is entered current should drop to an area of 50 millivolts . The fuse with the higher voltage drop will direct the tech to the problem area. Don't know your background so shouldn't get into anymore detail.

Have heard of Powertrain control module doing things like this after lightning strikes close by, required replacement.

 

Thank you I will try the suggestion. I am also worried the PCM was damaged

 

Good start point would have the DTCs read if any are present. With Charge Lamp On, there may be a code/s stored with a Smart Charge system.

Quick check,, after its run and been un-cabled for the night, next morning connect the cable but don't turn the key On/start/drive. With it cabled for 30-60 (or less) place your hand on the Alt case, is is warm?