04 fiesta zetec wont start-?

left ignition on and flattened battery, used jump leads to jump it from my van but wouldnt start, fan, lights, radio , windows etc all working but wont turn over, looked in manual and appears the immobilizer has armed and wont go off, i have since tried all sorts, locking and unlocking, disconnected battery, booster pack on battery but syill wont dis-arm, when jumping i accidently put on wrong terminals but was only for seconds and as i said everything else is still working so hoping its not that, i am going mad here, help!