My battery went dead and now when I try to charge it the car alarm goes off. I didn't even know I had an alarm. I have no remote to activate it.

It is possible that the car's alarm/immobilizer system is preventing the vehicle from starting. Manufacturers, in an effort to prevent car theft, have the immobilizer activate if the battery circuit is interrupted for more than a certain number of minutes. This keeps car thieves from cutting battery cables to prevent alarm activation. If the battery goes flat-line dead, the same thing can occur. You need a special tool available at a dealer or repair facility to reset the immobilizer.

Open the door,when alarm goes off insert key into ignition and alarm should go off and it should start,try that.

No, a car alarm will not go off if the car alarm is dead. -------------------------------------------------------------------------------
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check for a bad connection like a bad ground at the battery, make sure both terminals are tight at the battery, the starter and the ground at the engine. the shop that installed the EGR should have erased the codes, after 50 to 100 miles you would be able to go through emissions.

Have you tried disconnecting the negative terminal from the battery post and waiting about 20 minutes before reconnecting it.

Your Sonata is equipped with a "Keyless Entry & Burglar Alarm" system. When the Burglar Alarm is activated, it KILLS the starting system through the used of a relay called the "Burglar Alarm Relay". This mode prevents engine starting with the key.
Solution #1
Disarm the system with the Keyless Remote (key fob) If you don't have this remote (or its battery is dead) replace the battery & try disarming again.
Solution #2
Enter the vehicle & insert the key in the ignition and turn the ignition switch to 'RUN'. Wait 3 to 5 minutes until the alarm stops. You should then be able to start the engine.

Have a qualified/certified Hyundai Service Technician properly diagnose this issue.

if the batter has a drain the starter may be at fault the starter can drain a battery with out running i would unhook the battery cables then charge the battery then i would have the starter tested.

Disconnect the fuse for the alarm system or unplug horn relay system to change battery if you unplug fuse you will have to reset the alarm, be sure you know how to do this before disconnecting the fuse to the alarm system. Hope this helps.

check remote batt..if that dont work unhook car batt for 24 hrs. should reset

Take it to a garage and have them check the starter motor, alternator and battery. This problem sounds like it could be a seized starter motor but it could be a dead battery.