A peaceful island vacation. After everything they had done for Equestria, Princess Celestia decided to send Twilight and her friends to a tropical island retreat, off the coast of the zebra homelands. But after an encounter with a large group of slaver pirates, Twilight and her friends find themselves stranded on an uncharted jungle isle, engulfed in a war between the pirates and the natives. Separated from her captured friends, Twilight's only choice to rescue them is to learn the ways of the ways of the island and "awaken the warrior within her."

While I don't consider this a legit 'crossover', it's based off Far Cry 3.

After a thorough study of Nightmare Night, Twilight Sparkle brings forward questions of her studies to Princess Celestia, who gives her a mysterious books in hopes of answering her questions.