my headlights and wipers don't work right

On the Malibu, are the wipers and lights all on the same switch? If so, I would replace the switch. If you have a needle tester, turn on the lights or wipers and stick the needle into the wire. If the light doesn't come on, you know the switch is not operating. Your OBD tester must be acting as the switch when you plug it in.

but it will still control the running lights

Do you have daytime running lights? Do they come on when you start the car?

if the scanner is plugged in

If relays, fuses, and grounds are all good, the only thing I can think of would be the switch. Here's a video of how to replace. Really simple to do. https://www.youtube.com/watch?v=pR8NmTJ3QVI

it wasn't grounding right and when I pluged the OBD in it caused a full ground circuit

My running lights came on last night (on their own) & this morning the wipers came on (by their self) & the batter is now dead!!