Left lights on ,and ran down battery. When i try to jump start, alarm goes off,key fob wont work till battery charges tried putting key in ignition and turning key, tried locking and unlocking door. what do i do?

Push the lock button on your key fob for three seconds, until the lights on your dashboard blink. Your key has been reprogrammed, and your alarm and computer have been reset. Turn your Kia off, remove the jumper wires and close the hood.

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Try removing the alarm system relay, some car alarm has also a fuse on the alarm that you can remove.
Many car alarms unlock by inserting and turning car key while you connect the battery.

You could try disconnecting battery, leaving overnight and then inserting ignition key and switching on before reconnecting the battery.

It has sometimes worked for me but in reality it seems you probably have an alarm immobiliser fault you need specialist help with.

put key in ignition turn to number 2 and press the fob buttons open close etc. see if that reset system. also if you charged the batter while on the vehicle you can only charge them with a tried and tested charger from mercedes as you can damage the engine management unit and the voltage control module fitted to the vehicle. failing that you will need to remove the negative lead on battery and leave off for an hour or so. and reconnect, the alarm will still go off until its internal battery goes flat ruf 30min or so. when reconnecting battery make sure the doors are all unlocked and boot is unlocked, you also will need the code for the radio and other units that can be in the vehicle from manufacture. if this does not work then you may need another unit to replace before the engine will start again as it has been damaged. when battery connected sit in the vehicle and turn ignition to number 2 and press fob to lock unlock doors then try to start engine if all goes well the engine and alam will not be a problem anymore

engine management should read the transponder chip in your key and deactivate the alarm the battery in the key is charged while key is in ignition if the key hasn't been used for a while maybe its flat

The 2003 Sonata is equipped with a 'starter KILL' burglar alarm system with disables the starting system (using a N/C 'contacts' configuration instead of a N/O contacts configuration). N/C=Normally closed, and N/O=Normally open contacts. When the alarm goes off with a MY Sonata, the only way to DISARM it is with the key fob (remote) originally programmed for it (unless you purchase a new remote & have it programmed for the vehicle at an authorized Hyundai Service Department). NOTE: So long as the keyless entry & burglar alarm system is functioning/operating normally, the alarm will keep going off and the STARTER KILL function will still prevent you from starting the vehicle. One option is left without purchasing a new remote and having it programmed.
1. When the alarm goes off, get into the vehicle and insert the ignition key into the ignition.
2. Turn the key to the 'RUN' position (NOT the ACC position) and wait for the alarm to STOP (usually about 3 to 5 minutes).
3. The engine should then start using the ignition key.

If this procedure doesn't work, the problem will need further diagnosis by a qualified/certified Hyundai Service Technician.

Hope this helps

I take it the key fob doesn't work Try disconnecting the battery for 30 minutes and see if that will reset the alarm. You may need the key fob to reset.

If you hook up the jumper cables can you disable the alarm with the remote?

change the battery's in the key fob

Yes the key needs to be reprogramed to the car. Unfortunately that will have to be done by the dealer. Make sure that you have plenty of proof that you are the owner. They will reprogram it but you will not take posession of the car until you prove it is yours.