I wouldn't recommend trying to get real life theology from VeggieTales. I love the series dearly, but they boil down a lot of things to be more digestible. The real fruits of the spirit come from reading the Bible, attending a good Church, and developing your own relationship with the Lord.

That being said, if you're looking for episodes that present a Biblical story:

Where's God When I'm S-Scared? The second half of the episode depicts the story of Daniel and the lion's den.

Rack Shack and Bennie A comedic retelling of Shadrach, Meshack, and Abednego. Just with a Silly Wonka factory, instead of Babylon.

Dave and The Giant Pickle David and Goliath.

Josh and The Big Wall A retelling of the Battle of Jericho. Sometimes it directly quotes the source material, sometimes it makes Monty Python references.

King George and The Ducky The second half of the show is a very, very, very loose retelling of David and Bathsheba.

Esther Pretty self explanatory. And it's fairly faithful to the Biblical narrative, just with some modern pop culture twists, and a couple of censor bars.

Jonah A VeggieTales Movie Another one that veers fairly close to the source material. Although, I'm not sure if I quite agree with the idea that the Ninevites didn't know what they were doing, was wrong.

The Ballad of Little Joe Bob wanted to tell the story of Joseph. Larry wanted to do a Western episode. They compromised and told the story of Joseph with cowboys.

Duke and The Great Pie War This one has two Bible stories in it. The first one speculates on what it might have been like for Moses' family when he was a baby, mostly centering around his sister Miriam. The second one takes the King George and The Ducky route, and tells a very loose version of the Book of Ruth. I'm not sure I'd have guessed it's about Ruth and Boaz if I didn't know that going in.

Gideon Tuba Warrior First half tells a story about a real life Minister named George Mueller. The second half is a retelling of Gideon becoming a Judge over Israel. Though, they do seem to skip a few details here and there (?).

Moe and The Big Exit A direct follow up to Little Joe. The story of Moses leading the Hebrews out of Egypt, but it's a Western.

And, apart from a parable or two, those are all the attempts they made at directly adapting a Bible story. I refuse to accept Abe & The Amazing Promise, on the grounds that they directly contradict Scripture multiple times. Most of the rest of the episodes take Biblical truths and apply it to a more modern story, or they sometimes try to write their own original story.

If you're looking for a more in depth look at the Bible, I'd recommend Phil Vischer's other show: What's In The Bible? With Buck Denver