Applejack cries in the box underground all by herslef and no one hears her yelling. "Help! HELP!" She cries and hits the wall of the box. She thinks about Scootaloo who is also orange like her and the thought brings a smile to her face but she's still crying because sad. "I wonder what she's doing right now?" She wonders.
She continues to wonder this for days as she's frantic and unable to escape the box. Just enough air comes in through the box to make sure she doesn't die of air loss again but she eventually runs out of water and dies because it didn't raid for a whole week thanks to the pegasi who control the weather being lazy!
BAD END: Applejack died slowly and painfully in a small box underground. She didn't have room to run and wasn't able to buck trees for a last time before eventually die.
Scootaloo later exhumes the body and brings her dried remains in to class for Show and Tell