Anti theft activated after leaving code reader connected for a few hours which drained the battery

Hello guys, me and my mother were checking some codes on her vehicle and we saw that there were no trouble codes so we unplugged the device and left the car as is and hour goes buy maybe 2-3 and we try to leave and the battery’s drained. So we connect a jumper and give it power and wait a while and try to turn it over it cranks but stops mid crank. I believe it is the anti theft system, but how do I disable this?