The Persimmon Tree opens in Indonesia in 1942 on the cusp of Japanese invasion and the evacuation of Batavia (Jakarta) by the Dutch. Seventeen-year-old Nicholas Duncan is on holiday there, in pursuit of an exotic butterfly known as the Magpie Crow. It's an uncertain, dangerous time to be in Indonesia, and Nick's options of getting out are fast dwindling. Amidst the fear and chaos he falls in love with Anna, the beautiful daughter of a Dutch acquaintance, and she nicknames him 'Mr Butterfly'.

To assist in the escape, Anna's father gifts Nick his prized yacht, Vlermuis, to sail to Australia. Singapore has just fallen, the Japanese have made it to Sumatra, and the waters are dangerous. Vlermuis is not long out of Batavia when Nick is forced ashore for repairs. He witnesses the bloody execution of shipwrecked Allied soldiers by natives, and while burying what's left of the bodies Nick notices one wounded soldier has escaped death, and he carries him back to his yacht. The rescued soldier is a lower-class Irish Catholic American called Kevin Judge. He has no sailing experience, but he assists Nick in navigating through some dramatic storms and the two form an unlikely and lifelong friendship.