Car alarm

Car alarm was set, my friend  unlocked the
passenger door  threw open window ,  and alarm
went off ,she didnt hav the remote or keys to
disarm it and it stoped when battery died , i was
gone for a couple days out of town so when i
returned i had the fob and keys ,now with dead
battery ,opened hood found that neg cable also
was off ,  so when i attached neg cable  to charge it
a clicking sound was comming from the dash so i
dissconnected the neg and charged up the battery,
next am I put the neg cable bac on and alarm
started to sound I tried to press the car remote and
it didnt stop it is there some other way to reset this   
so i can stop alarm and start my car thank u