Jonah was a major prophet in Israel (the Northern Kingdom); according to the Midrash (Pirkei Rabbenu Ha-Kadosh) he was a disciple of Elijah. The Assyrians (whose capital was Nineveh) were the major threat to the Northern Kingdom. Malbim's commentary on Jonah 1:1 suggests that Jonah was sent to prophesy destruction to Nineveh because G-d knew that they would then repent and become more worthy of being G-d's agents to punish Israel.
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