31 Mpg. Rattle engine knock only on low battery charging.

I dont know what is causing my misfire, but after a while of driving I found out that the rattle my vehicle has only comes on during when my battery level on my dash shows at 2 bars. That is when the engine and transmission shakes and vibrates the car uncontrollably and makes a loud noise.
If I put it in neutral, the vibrations and noise stops but then the battery does not get charged. I have to put my foot on the brake and have to floor the gas pedal to force charge which produces no vibrations or rattling since my engine rpms get higher.
If i am driving at low speeds with low battery, it also vibrates and rattles but to a lesser degree.

When the battery is 3 bars or higher, i dont experience any rattle or vibration while stopped with the engine running.

Im also getting in the low 30s gas mileage which kinda ruins the point of driving a prius.

Is my crankshaft broken or something?