How God Dealt With Jonah as a Prodigal When He Ran From God
But Jonah arose to flee to Tarshish
from the presence of the Lord.
Jonah 1:3 (NKJV)
The book of Jonah recounts a time in the life of the prophet Jonah when he became a "prodigal" for a time. I am defining a prodigal as one who knows God but, for whatever reason, has walked (or ran) away. I think of those who, at one time, was on fire for the Lord, but something happened, and now they are attempting to run from God. I want this story to remind you that God is still in control; He is sovereign over His creation. "Although Jonah is the main character, the book's main purpose is not to teach us about him but to teach us about God. Through Jonah's experience, God, the all-powerful Creator, reveals that though he is a God who will pour out his wrath on the wicked, he is also one who eagerly pours out his mercy on those who repent--including those we would too quickly deem to be beyond mercy." 
THE STORY OF GOD AND JONAH
At the beginning of the story, the word of the Lord came to Jonah, saying, "Get up and go to the great city of Ninevah. Announce my judgment against it because I have seen how wicked its people are" (Jon 1:2). Instead, Jonah got up and went in the opposite direction to get away from the Lord. We don't learn until later why Jonah didn't want to obey; that he knew God wanted to be merciful and that the people would repent (see Jon 4:2). Jonah didn't want to see Ninevah spared, and because God was willing to spare them if they repented, he was angry.
God came to Jonah because He is a God of mercy (Jonah 1:1-3). Jonah was one of God's prophets, meaning he spoke for God to the people. God saw how wicked the people of Ninevah had become, and since God must punish sin unless there is repentance, He wanted to give Ninevah a chance to repent. So He sent Jonah to warn the people, but Jonah didn't go. Jonah went, instead, in the opposite direction to Joppa, found a ship headed to Tarshish, and got on the boat, hoping to escape from God's presence.
Jonah ran from the presence of the Lord, but God was still there. It is futile to run from God because God is everywhere. In Psalm 139:7, David asks, "Where can I go from Thy Spirit? Or where can I flee from Thy presence?" He concludes it's impossible to escape because God would be there no matter where he might go (v 8-12). David wasn't trying to run from God as Jonah was; rather, he was expressing his awe at the Lord's omnipresence. Surely Jonah knew this about God, but in his anger, he acted inconsistently with what he knew to be true about God. Acting inconsistently with what they know to be true could be true of any prodigal.
God made His presence known to Jonah and the sailors (Jonah 1:4-12). While sailing to Tarshish, the Lord sent a great wind and a powerful storm that threatened to destroy the ship. The sailors were frightened and began crying out to their gods. They threw the cargo overboard to lighten the load, but the storm kept up. Jonah was sleeping below and oblivious to what was going on. So the captain found him and asked, "How can you sleep at a time like this? Get up and pray to your god. Maybe he will pay attention to us and spare our lives" (v 6). The crew then cast lots,* and the lots identified Jonah as the culprit. "Who are you?" the sailors demanded, "What is your occupation? What country do you come from? What is your nationality? What did you do to make your god so angry?" Jonah replied, "I am a Hebrew, and I worship the Lord, the God of heaven, who made the sea and the land." This frightened the sailors even more because Jonah had already told them he was running from God. "Why did you do it?" the sailors pleaded; "What should we do to you so this storm will stop?" Jonah knew the answer, "Throw me into the sea, and it will become calm again."
Jonah recognized he had not outrun God. His disobedience was the reason God had sent the storm. Oh, how small he must have felt when the truth finally hit him. How had he been deceived? God will not be mocked. A person reaps what they sow (Gal 6:7). Nothing in all creation is hidden from God. He sees everything, and He is the One to whom we are accountable (Heb 4:13). All he could do now was tell the sailors who this God was that he worshiped, take responsibility for his disobedience, and tell them what they needed to do for the storm to end. But he couldn't have known what would happen next!
God was not finished with Jonah or the sailors (Jonah 1:13-17). The sailors didn't want to throw Jonah overboard; surely that was too drastic a thing for Jonah's God to ask. So, they rowed even harder to get the ship to land. But it didn't take long for them to know the storm was much too violent for them, and there was no way they could make it. They cried out to the Lord, "Please don't make us die for what this man did, and don't hold us responsible for his death. You sent this storm for your own reasons." Then the sailors picked up Jonah and threw him into the raging sea, and the storm stopped at once! Verse 16 tells us, "The sailors were awestruck by the Lord's great power, and they offered him a sacrifice and vowed to serve him." Meanwhile, in the raging sea where Jonah had just been thrown, God arranged for a great fish to swallow him. "And Jonah was inside the fish for three days and three nights." This part of the story ends with the sailors now serving the one true God and Jonah still alive.
Jonah may have thought he knew what would happen when he was thrown overboard, but God had other plans. God is in control. Not only are His thoughts and ways higher than our thoughts and ways (Is 55:8-9), but the Bible tells us that even though we make our plans, or in Jonah's case, think we know what will happen, "the Lord determines our steps" (Prov 16:9). Jonah was not successful in running from God, and when he probably thought he would die in the water, God had something else in mind.
God has mercy in response to Jonah's repentance (Jonah 2). From inside the fish, Jonah turned to God. He may have written his prayer after the fact, but it's clear he was crying out to God while in the belly of the fish. "I cried out to the Lord in my great trouble, and he answered me. I called to you from the land of the dead, and Lord, you heard me!" Jonah begins to recount what had happened (v 3-6), and as his life was slipping away, he remembered the Lord (v 7). Much like the sailors had done in response to God's greatness when He stopped the storm, Jonah promised to offer sacrifices and songs of praise and to fulfill all his vows (v 9). I assume that meant Jonah would obey God if God asked him to go to Ninevah again. If repentance is a changing of your mind, then Jonah was changing his mind about disobeying God and being able to outrun Him. And that's when the Lord ordered the fish to spit Jonah out onto the beach.
God spared Jonah's life and told him again to go to Ninevah. This time Jonah obeyed. The rest of the story is for another time.
God does not deal with all prodigals the same way. He knows each one intimately and will do what works best. Sometimes it is a storm and a great fish (something unique and unlikely), and we should look to Jonah's story for hope rather than praying God will remove the storm or keep it from coming.
If you have a prodigal who is running from God, and God is getting ready to send a storm, that means your prodigal is either on their way to Joppa, in Joppa looking for a boat that will take them farther away to Tarshish, or on the ship sleeping. They haven't yet been thrown into the water or even had a chance to acknowledge God sent the storm, and they haven't been swallowed by a fish. It's important to understand that they are in the in-between time of going in the opposite direction to get away from God and admitting God is still there. Sometimes our prodigals will be in this place for a long time, much longer than Jonah was. It is God's timing, and the story of Jonah can only give us something to hold on to. At this point, a prodigal hasn't yet repented, which is necessary for God to enact His mercy on them. He has already shown them some mercy by giving them someone who is praying for them and not giving up on them. God, Himself is not giving up on them. God didn't give up on Ninevah or Jonah. In fact, in this story, Jonah is restored, and Ninevah is saved. I could do another blog on God's mercy to Ninevah (the rest of the story), an unsaved nation who was an enemy of Israel.
If you have a prodigal who is running from God, and God has already sent the storm, that means your prodigal has the opportunity to speak up and acknowledge it is from God. Jonah's storm involved sailors who didn't know anything about Jonah's God, and God used the storm and Jonah to bring others to know Him. Any storm God might send into the life of your prodigal is a chance for them to acknowledge God and, in turn, point others to Christ, even before repentance. We should not pray for there not to be a storm. If that is what will bring others to Christ and be the catalyst for our prodigal to repent and be shown God's mercy, then we should instead see the possibilities of the storm sent by God.
If you have a prodigal who is running from God, and God has sent a "fish to swallow them," that means they have probably acknowledged God sent the storm, but they have yet to repent because they don't realize the storm will not be their end. I have no idea what the "fish" might look like, but it will be the result of the storm and God's intervention after they have acknowledged Him. It will be for the purpose of your prodigal repenting. Don't expect to know everything that is going on. We rarely see things from God's perspective, and often our prodigals will not want to tell us the details of their journey back to God while they are in it. They may not even understand it all yet. I remember reading some advice from a former prodigal that affirmed they would probably not want to disclose their first attempts at returning to God for fear of disappointing those who love them and are praying for them, in case it doesn't work out. So don't be discouraged.
For Jonah, it took one storm and one fish. No one can promise that will be the case for your prodigal. But one Scripture I find encouraging is Luke 18:6-8, where Jesus is telling us what we are to learn from the parable of the persistent widow and the unjust judge (Lk 18:1-5). Jesus says, "Learn a lesson from this unjust judge. Even he rendered a just decision in the end. So don't you think God will surely give justice to his chosen people who cry out to him day and night? Will he keep putting them off? I tell you, he will grant justice to him quickly!..." The word quickly does not necessarily mean immediately but will happen speedily when the answer begins to come. 
That's why the parable was told...to show that at all times to pray and not lose heart or give up. We have to persevere while our prodigals are still running until they repent and receive God's mercy of restoration. None of us knows how long we will have to persevere in prayer, but we can find encouragement in knowing God loves us, He loves our prodigals, and He loves justice! His promise here is that He will surely give justice to His people who cry out to Him day and night, and when the answer comes, it will happen quickly! If we raised our children to know the Lord and believed and saw with our own eyes them accepting the Lord as Savior, then I would say God wants to give us the justice of seeing them restored to faith. I am not proposing we can know with certainty that our prodigals will return to the Lord because that is not what the verse says. We can only know that He will give us justice. God will provide our prodigals every opportunity to see Him as a God of mercy and that they can't outrun Him because He is wherever they are; that He is not finished with them, but it will mean repenting and doing things His way.
Do you have faith to believe God will do what He says He will do?
 Introduction to the Book of Jonah: NLT Study Bible 2008
 Note on Luke 18:8: NASB Study Bible 1976,1978
*Casting lots was writing names on small stones and putting them in a container, then taking one stone out, or letting it fall out, to determine what they were trying to figure out. In the story of Jonah, the sailors were using this practice to determine who was responsible for their god sending the storm. It was fairly common in the ancient world to assume that when something bad happened, it was due to some god being offended. Casting lots was a popular form of divination used by both the pagans and the Hebrews. Although divination, in general, was displeasing to the Lord, God allowed lots for specific purposes (see Lev 16:8; Josh 18:6; 1 Sam 14:42; 1 Chr 26:12-16; Neh 10:34; Acts 1:26). What appeared to be by chance was really part of God's sovereign design (Prov 16:33).
(information gathered from notes on Jonah 1:7-8 NLT Study Bible 2008; Jonah 1:7 & Proverbs 16:33 NASB Study Bible 1976,1978)