Be aware that it may already be too late. Once the power is cycled with a dead battery, the proto one system can get its brain scrambled.
You can usually fix that with a special repair chip that MTH makes and sells to anyone.
If the loco is proto two, usually no harm is done, but you still need a battery or a BCR to make the train run.
You can use any 9 volt battery to test the system, but only leave the correct rechargeable, or a BCR in the loco.