In the sequel, Applejack was never there.
A popular hypothesis is that Twilight and her friends were racked with guilt about what happened to Applejack and the lies that they'd told. "Applejack" was a hallucination brought about by their paranoia (and possibly drinking the sleep-preventing potion themselves).- Confirmed. All of Applejack's encounters were hallucinations induced by Apple Bloom via potion gas.
Apple Bloom is still alive, and she wants revenge.
A less well-known idea is that Apple Bloom, whether Applejack escaped or not, knew about what really happened. With her potion-making skills, she would recreate the potion to make the other five suffer from what her sister went through.- Confirmed.
