Once completely dead a 100% discharged battery will need a slow charge to bring it back. 24-36 hours is not uncommon but sometimes they are just too far gone.
might want to check the battery with the car off and see if it has a drain, for some cars you will need to wait 20 minutes or so to wait for the ECU/DME to go into "sleep" mode (there timers/delays in some circuits). After the 20 minutes or so you will have your actual drain. see how many milliamps it is drawing, the alarm and blinking light do drain some but not enough to kill the battery.
Another thing, long gone are the days of the single wire alternators, today most high end cars even some in the 80's to now have an exciter wire or communication intarface wire that either goes from the ECU or to the gauge cluster, if this wire is no good due to a rodent chewing on it well, the alternator will not charge.
Last but not least, MAKE SURE YOUR GROUND AND ENGINE GROUND ARE GOOD!