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Why did Yonah Run Away?
The Story of Jonah and the Fish in a Nutshell, from Chabad.org
The story of Jonah is one of the more intriguing and enigmatic stories in the Bible.
A prophet named Jonah is commanded by G‑d to warn the people of the Assyrian city Nineveh of their impending destruction if they don’t repent of their wicked ways. Instead of gladly following G‑d’s command, Jonah tries to “escape” from G‑d and hops onto a boat heading in the other direction. When sudden storms threaten to sink the ship, the sailors determine that someone on board must be at fault. They cast lots, and the lot falls on Jonah. Jonah tells them he is at fault for running away from G‑d and they should throw him overboard. A miracle happens and a large fish swallows Jonah alive. While in the belly of the fish, Jonah prays to G‑d for three days and eventually agrees to fulfill his mission. The fish spits Jonah out, and he goes to warn the inhabitants of Nineveh, who then repent of their sinful ways.

(א) וַֽיְהִי֙ דְּבַר־ה' אֶל־יוֹנָ֥ה בֶן־אֲמִתַּ֖י לֵאמֹֽר׃ (ב) ק֠וּם לֵ֧ךְ אֶל־נִֽינְוֵ֛ה הָעִ֥יר הַגְּדוֹלָ֖ה וּקְרָ֣א עָלֶ֑יהָ כִּֽי־עָלְתָ֥ה רָעָתָ֖ם לְפָנָֽי׃ (ג) וַיָּ֤קָם יוֹנָה֙ לִבְרֹ֣חַ תַּרְשִׁ֔ישָׁה מִלִּפְנֵ֖י ה' וַיֵּ֨רֶד יָפ֜וֹ וַיִּמְצָ֥א אָנִיָּ֣ה ׀ בָּאָ֣ה תַרְשִׁ֗ישׁ וַיִּתֵּ֨ן שְׂכָרָ֜הּ וַיֵּ֤רֶד בָּהּ֙ לָב֤וֹא עִמָּהֶם֙ תַּרְשִׁ֔ישָׁה מִלִּפְנֵ֖י ה'׃

(1) The word of the LORD came to Jonah son of Amittai: (2) Go at once to Nineveh, that great city, and proclaim judgment upon it; for their wickedness has come before Me. (3) Jonah, however, started out to flee to Tarshish from the LORD’s service. He went down to Joppa and found a ship going to Tarshish. He paid the fare and went aboard to sail with the others to Tarshish, away from the service of the LORD.
לברוח תרשישה . ים ששמו תרשיש והוא בחוצה לארץ אמר אברח לי הים שאין השכינה שורה בח''ל אמר לו הקב''ה חייך יש לי שלוחים כיוצא בך לשלוח אחריך ולהביאך משם משל לעבד כהן שברח מן רבו ונכנס לבית הקברות אמר לו רבו יש לי עבדים כיוצא בך לשלוח אחריך ולהביאך משם ומה ראה יונה שלא רצה לילך אל נינוה אמר העכו''ם קרובי תשובה הם אם אומר להם ויעשו תשובה נמצאתי מחייב את ישראל שאין שומעים לדברי הנביאים :

to flee to Tarshish: I.e, to a sea named Tarshish, which is outside the Holy Land. He said, “I will flee to the sea, for the Shechinah does not rest outside the Holy Land.”

Said the Holy One, blessed be He, to him, “By your life, I have messengers like you to send after you and fetch you from there.” This is illustrated by an allegory of a priest’s slave who fled from his master and entered a cemetery [making it impossible for his master to retrieve him]. His master said to him, “I have slaves like you to send after you and fetch you from there.”

Now what did Jonah see that he did not wish to go to Nineveh? He said, “The gentiles are quick to repent. Should I prophesy to them and they repent, I will be found condemning Israel, who do not heed the words of the prophets.” [from Mechilta, Exodus 12:1]

Ibn Ezra bolsters this explanation from the language of the Pasuk. He notes that Yonah did not seek to escape “MiPnei Hashem,” “from Hashem”, rather “MiLifnei Hashem,” “from the presence of Hashem” (Yonah 1:3). Yonah did not think he could elude Hashem and instead sought to simply “step out of Nevuah range.” Yonah perceived Chutz LaAretz as what we would call “out of bounds”, out of the playing field, so to speak, of prophecies about Nineveh25See Moed Katan 25a and Sefer HaKuzari 2:14 for an explanation why certain Neviim such as Yechezkeil received prophecy outside of Eretz Yisrael. .
Does Yonah Actually Think He Can Flee God? By Rabbi Haim Jachter
We suggest that Yonah’s ill-fated attempt to flee from God’s jurisdiction is the perfect description of the mindset when people sin. People sometimes think, quite irrationally, that they can act independently from God. Most often, though, they fail to think at all. Had people properly thought out their behavior they never would have disrespected God’s will.
Chazal teach (Rashi to Bamidbar 5:12 s.v. Ki Tisteh Ishto citing Midrash Tanchuma Bamidbar 5) “Ein adam chotei ela im kein nichnas bo ruach shtut, a person sins only if overcome by irrational thinking.” However, the objective observer, similar to readers of Sefer Yonah, recognizes the irrationality of a sinful act. The sinner, on the other hand, caught in the throes of his misdeed, fails to recognize the foolishness of his act.
How to explain, for example, people who are piously meticulous in prayer at the synagogue and Torah study in the beit midrash, yet act reprehensively when at their place of business? Why do people who would never dream of eating anything that comes even remotely close to non-kosher log on to foreign and forbidden sites on the internet or view a movie that is not fitting to watch?
Sadly, such behavior may be explained as people irrationally viewing certain areas of life as “religion-free” or “God-free zones.” Just as Yonah thought he could escape into a God-free zone by leaving the Land of Israel, so too those who violate God’s laws thoughtlessly and foolishly delude themselves into thinking that a God-free zone exists. On Yom Kippur we are expected to take a good, hard look at our lives and examine our actions and deeds. Our bird’s-eye view into the absurd behavior of Yonah should grip us, bring us back to our senses, and help us avoid such counterproductive, self-destructive and self-sabotaging violations of God’s laws.
Yom Kippur is a day when we immerse ourselves in holiness and remove ourselves from our usual human urges. This allows us to reboot and reset our behavior so as to act in better ways after Yom Kippur is over. Sefer Yonah plays a critical role in our rebalancing, rebooting and reimagining our lives. It leads us to realize our potential to achieve spiritual excellence.
Yonah is most likely motivated to flee God due to his anger at God for adopting too lenient judgment of mankind in general, and Nineveh specifically. His flight to Tarshish to elude God’s presence is senseless, perhaps spurred on by his anger. Our recognition of the senselessness of Yonah’s actions has the potential, especially on Yom Kippur, to guide us back to act in a sensible, wholesome, and constructive manner. A manner in harmony with, and not in conflict with, the loving God whose every command is issued to serve our best interest.
Sefer Yonah communicates to us readers on Yom Kippur to have a look from outside of ourselves. We can see the behavior Yonah is overlooking and we must make sure not to overlook similar behaviors in ourselves.

אברבנל יונה ב'

אמתת הענין הוא שיונה נתחרט ממה שברח מלפני השם וגמר בלבו לעשות מצוותו בענין ננוה אבל היה מתנחם באומרו שאנשי ננוה שהם משמרים הבלי שוא אף על פי שיעשו תשובה מפני קריאתו לא יתמידו בתשובתם כי לימים מועטים חסדם יעזובו וישובו לרשעתם

Abarbanel Yonah 2

The truth of the matter is that Yonah regretted fleeing HaShem and promised in his heart to fulfill His command regarding Nineveh. But he was comforted in his realizing that the people of Nineveh were worshippers of nothingness and, so, even if they did Teshuva because his call, they would not be steadfast in their repentance— after a few days, they would leave their righteousness and return to their evil

Yonah’s Gourd: What Can It Teach Us About The Teshuva Process? By Dr. David Bar-Shain
Year after year, we stand in shul on Yom Kippur and regret the same actions, say the same words, and resolve to improve the same deficiencies. Even if we do manage to make changes, we know that it’s likely that we will relapse. A cynic could make the reasonable observation that our resolutions are weaker than our temptations, and the prediction that, no matter how sincerely we confess and try to do better, it is very likely that next year we will be confessing the same sins and making the same attempts to change.
When חז"ל chose Sefer Yonah as the Haftorah for Mincha of Yom Kippur, they made an inspired choice. On the surface, the story is a simple story of rebuke, change, repentance and forgiveness. My approach to finding meaning in Sefer Yonah emerges from [the observation that], Yonah is unhappy that God rescinded the decree because he doesn’t think that their repentance was sincere and would be long-lasting.
I’d like to read the story as showing that, in contrast to Yonah, God values sincere change no matter how briefly it lasts. Yonah is angry at God because Yonah doesn’t believe that the people of Nineveh have made efforts which will bring lasting changes to the moral fabric of their society. Yonah’s anger that God forgave the people anyway may be understandable in light of Yonah's concern for his reputation (if the destruction that Yonah prophesied doesn’t come to fruition, then he might be viewed as a false prophet), or in light of his concern for Bnei Yisrael (who might look bad when contrasted to the people of Nineveh, or who might later lose in battle to the people of Nineveh).
The message of Sefer Yonah is that if our resolution to change is sincere, God is willing to partner with us and give us another chance. This fresh beginning can lead to great optimism. Further, Sefer Yonah teaches us that dwelling in isolation from the world and its temptations is a means to self-change but not an end in and of itself. At some point, God will remove his support (the kikayon tree withers and dies) and we will be left with whatever changes we have succeeded in securing into place.