The story of Jonah is one of those Scripture passages that we as Catholics would say is a TRUE story, but not necessarily FACT. Catholics believe that everything in the Bible is TRUE in a religious sense. However, when it comes to scientific and historical truth (facts), there are times that the Bible is not totally accurate.
Why? Simply because the Bible comes to us from a time when most people were not literate and certainly not as literal as we are today. They did not have science and history as we understand those fields today. So, although there is a great deal of historicity in the Bible (proven by archeological study), we also find that there are places where figurative language was used. Figurative language (for example: “it’s raining cats and dogs”) expresses truth without relying on fact. In the case of the story of Jonah, we are not to concern ourselves with the physics of the situation (i.e. proving that a human can live in the belly of a large fish for three days), however, we are not to dismiss the story either as a fairy tale. It is a TRUE story: teaching us the truth of what happens when we seek to follow our own desires instead of following the will of God. When we ignore and run from God’s will, we eventually find ourselves in the “belly of the whale” — that place of darkness where we cannot see what direction to go in. As soon as Jonah concludes that he should say “yes” to God’s call, he sees the light of day.
All of us either have been or will find ourselves in the “belly of the whale.” This story teaches us the key to avoiding this dark place as well as the key to freeing ourselves from such darkness so that we can see the light. For a good understanding of how Catholics are to read and interpret the Bible, see the document The Interpretation of the Bible in the Church published by the Pontifical Biblical Commission (especially sections IF, IIB).