2002 Jeep Grand Cherokee alarm system problem

2002 Jeep Grand Cherokee mileage: 75,000. I disengaged the battery to check the water pump and after I hooked the battery back up, I noticed my alarm was "tweaking." I tried to take the Jeep to town, but it kept cutting out on me which is the anti-theft part of the alarm. How can I reset it to where I can drive the vehicle? I turned the valet switch off and then on, but nothing happened.