Many of the events and people of Jotham's Journey are based on the Bible.  Of course, the most important parts of the story center around the events of Christ's birth, as told in the Gospels.  But there are other references as well.  Here are just a few:

En Gedi - 1 Sa 23:29

Jericho - Nu 22:1, Dt 34:3, Jos 6:1, Jer 39:5, Mt 20:29, Mk 10:46, Lk 10:30

Dead Sea - Ge 14:3, Nu 34:3, Dt 3:17, Jos 3:16, Joel 2:20, Zec 14:8

Megiddo - 1 Ki 9:15, Zec 12:11

Elizabeth - Lk 1

Zechariah - Lk 1

Simeon - Lk 2:25

Anna of Phanuel - Lk 2:26

Essenes - while not mentioned in scripture, much is known about this sect through the writings of Josephus and other ancient historians.  They lived much as described in Jotham's Journey, forsaking marriage to devote themselves to God.

Qumran and the Scrolls - the "Dead Sea Scrolls" are not mentioned in scripture because they are scripture.  These scrolls are some of the earliest copies of much of the Old Testament.  As in Jotham's Journey, the scrolls were placed in urns and hidden in the caves outside Qumran for safe keeping.  It worked.  Qumran was destroyed shortly after the close of the New Testament, but the scrolls remained until finally discovered in about 1947.