An unprecedented divine command sets a perilous journey in motion, raising profound questions about providence, reward and punishment, and a prophet's dual loyalty to God and his people. God directs a Hebrew prophet to travel to the heart of a foreign empire, Nineveh, the capital of Assyria [אבן עזרא, שטיינזלץ]. Although they were a foreign nation, the people of Nineveh had revered God in the distant past. Only recently had they begun to corrupt their ways, prompting God to send a prophet to them [אבן עזרא]. The task requires him to voice God's call [רש״י], rebuking the city's inhabitants and warning them to abandon their evil deeds before disaster strikes [מצודת דוד, שטיינזלץ, מלבי״ם]. Even though he does not speak their language, the message is meant to cross linguistic barriers, easily understood by people who are willing to hear the words of a prophet [שטיינזלץ].
The catalyst for this mission is the sheer accumulation of their wrongdoing. Their evil deeds have piled up, ascending to the heavens and transforming into a powerful force that demands punishment [מצודת דוד, חומת אנך]. Typically, direct divine providence and the dispatching of prophets are reserved exclusively for the Israelites. However, when the nations of the world engage in violent robbery and corruption that threaten the very existence of a functioning society, God intervenes directly, just as He did during the generation of the Flood and in Sodom [רד״ק]. Furthermore, the sins of Nineveh generated such an intense accusation that they reached directly before God. While the transgressions of other nations usually only affect their designated heavenly representatives without disrupting the higher spiritual realms, the evil of Nineveh amplified to an exceptional degree [חומת אנך].
The primary approach among commentators is that a deeper intention lies behind this mission, one intimately connected to the Israelites. God wishes for Assyria to repent so that they will be worthy to serve as His instrument of punishment against a sinful Israel [מצודת דוד, מלבי״ם]. Additionally, the swift repentance of these foreigners is meant to hold up an accusing mirror to the Israelites, who stubbornly refuse to listen to their own prophets [מלבי״ם]. This understanding explains the prophet's famous refusal. He chose to protect the honor of his people over the honor of his Creator, refusing to participate in a sequence of events that would ultimately harm the Israelites or shame them in the face of gentile repentance [אבן עזרא, מלבי״ם, חומת אנך].
Another significant aspect of this mission is the ambiguity of the initial command. God instructs him to call out against the city, but at this stage, He does not provide a specific prophecy or a sealed decree of destruction. Instead, the prophet is merely tasked with delivering general moral rebuke [רד״ק, אבן עזרא, מלבי״ם]. This vagueness provided him with a legal justification for his flight. Because he was not sent to announce an absolute prophetic verdict, he reasoned that suppressing his message would only violate a positive commandment, sparing him the severe penalty normally given to a prophet who suppresses a direct prophecy [מלבי״ם]. Consequently, this dispels the notion that he fled out of fear of being labeled a false prophet if Nineveh repented and the disaster was averted. The people of Nineveh were wise enough to understand that the entire purpose of a prophetic warning is to inspire repentance and cancel the decree, so they never would have considered him a false prophet [אבן עזרא].