Allah reveals His message to His creation, in certain ways, and the Messengers are the instruments by which Allah carries out his Will.
“And indeed, Yunus was among the Messengers.” 
A story about hardship, patience, repentance and sincerity. One that will continue to capture the hearts of all those who read and extract wisdom from it. This is the story of the beloved Prophet Yunus (A.S.).
Nabi Yunus (A.S.) was born to Amittai in the town of Nineveh located on the banks of the Tigris River, North Western Iraq. He was sent by Allah to guide the people of his generation as they were idolaters who indulged in sin.
For a long time Prophet Yunus (A.S.) tried his best to convince these people to believe in the Oneness of Allah and to abandon idol worship. They mocked him and refused to listen, telling him that idol worship is what they have believed in for generations and that they had no intent to stop. Yunus (A.S.) warned them that if they persisted with their sin, Allah’s wrath would fall upon them. Instead, they continued with their mockery, even challenging punishment.
Feeling disheartened and frustrated Nabi Yunus (A.S.) left the town without realizing that Allah had not given him the command to do so. After a long distance, he finally reached sea and saw a boat with people in it ready to depart. Nabi Yunus (A.S.) appearing rather distinguished, was welcomed abroad the boat ready to set sail. All of a sudden, amidst the smooth sailing, a heavy storm diverged causing the boat to reach high proximity followed by steeping plunges down. They realized, that weight had to be reduced onboard in order for the boat not to sink. So they cast lots in order to reach a decision.
When the lot was drawn Nabi Yunus’s name appeared and so they decided that since he was so dignified they would choose again. The second time round, the name of Yunus (A.S.) was drawn again! They decided to cast lots one more time, but again, the name of Nabi Yunus (A.S.) surfaced and he was forced to be tossed into the sea. This is clear proof to us, that no matter how hard we try to do things according to our plans, Allah is in total control, and His plan will always be above ours.
The Belly of the Whale
All along a whale had been trailing the boat that Yunus (A.S.) had boarded. Allah commanded it, to find Nabi Yunus (A.S.) and swallowed him without hurting him or crushing any of his body parts. Nabi Yunus (A.S.) remained in darkness for a long time in the belly of the whale. His remembrance was constantly of Allah and his eyes filled with tears as he wept to Allah for forgiveness. He realized that he should not have left the town neither the idolaters as he had been sent as a Messenger of Allah, to lead them to the straight path.
Allah tells us in the Qur’an
" And [mention] the man of the fish, when he departed in wrath: and thought that We would not decree [anything] upon him. But he cried out within the depths of darkness, "There is no God except You; exalted are You. Indeed, I have been of the wrongdoers."
Allah accepts prayer of those who seek repentance.
Yunus (A.S.) constantly supplicated to his Creator and Allah accepted his sincere repentance, as we are told in the next verse of Surah Anbiyaa,
“So We responded to him and saved him from the distress. And thus do We save the believers.”
Meanwhile, back in Nineveh ..
Meanwhile, a dark cloud of fury displaying Allah’s wrath had already formed above the town displaying clear signs of the warning of Nabi Yunus (A.S.), when he would constantly warn them about the result of their disobedience.
When the skies began to change into a fiery color, the people of Nineveh remembered the story of their predecessors, the story of Nabi Nooh (A.S.) and they feared that they would gain the same fate. Immediately fear crept into their hearts and they kneeled down into prostration begging Allah for forgiveness. Their cries for repentance and for the return of their Leader Nabi Yunus (A.S.) echoed through the mountains and Allah the Most Merciful accepted their plea.
Allah Says, “When they prayed for Nabi Yunus (A.S.) to return to them and believed, their punishment was removed.” 
Through Allah’s command, the whale was told to eject Nabi Yunus (A.S.) onto the shore. His body was inflamed due to the acid in the stomach of the whale which now covered his body in pain. Allah is so Merciful, that He caused a plant to grow over Yunus (A.S.) thus covering his body from the sun and at the same time healing his burns as well as bearing fruit to sustain him.
Over a period of time Yunus’s (A.S.) flaccid state, gradually improved and He was commanded by Allah to return to guide the people of Nineveh.
When he returned, he was surprised to see that they had abandoned their idol worship and now believed in the Oneness of Allah. Nabi Yunus (A.S.) thereafter continued to prosper and guide the people of Nineveh until, just like every other human being he returned to Allah, the Almighty.
Yunus (A.S.) was known to have such a sublime character, that our beloved Prophet Muhammad (S.A.W.) forbid any of the Sahabah to ever say that He, Muhammad (S.A.W.) was in any way better than Yunus (A.S.). Such, was the love that our Prophet (S.A.W.) harbored for Yunus (A.S.).
As is stated in a Hadith Narrated by`Abdullah:
“The Prophet said, "None of you should say that I am better than Yunus (i.e. Jonah)." Musadded added, "Jonah bin Matta." 
The people of Nineveh shut their eyes to the message of Islam. They believed that false Gods would intercede on their behalf, but how can stones intercede on your behalf.
As Allah tells us in Surah Yunus that even the false Gods shall leave the idolaters and say,
“It was not us that you worshipped” .
These false Idols, were a mere figment of the imagination of those who believed in this false worship.
From this sincere story in the Qur’an, we learn that even the greatest of people, A Messenger of Allah, could become frustrated. While in the belly of the whale, Allah tested Yunus (A.S.) by seeing how much patience his heart possessed. Could you imagine being all alone beneath three layers of darkness, i.e. the darkness of being in the stomach of the whale, enclosed by the darkness of the deep ocean with deep blue sky encapsulating it all.
We must understand, that within this darkness we gain both a physical as well as spiritual moral. The physical darkness, refers to the darkness he could touch and see. The spiritual darkness refers to the dark feeling he felt in his heart, his distress, which he realized he had brought upon himself.
It is for this reason that Allah sent his Messengers as normal people to Mankind, in order that we may understand that everyone makes mistakes but our test is to seek sincere repentance and find our way back to Allah.
The beauty of this story, is that amidst the depths of darkness, Nabi Yunus’s (A.S.) heart filled with repentance and sincerity. As Allah’s servants, we learn that it is never too late to seek sincere forgiveness, because Allah, is the Most Forgiving, the Most merciful
 Quran 37:139
 Qur’an 21:87
 Qur’an 21:88
 Quran 10:98
 Sahih al-Bukhari 3412
Book 60, Hadith 85
Vol. 4, Book 55, Hadith 624