But the Lord
Now in one sense Jonah's story is over at this point. That is, the story of his choice, his disobedience, is over. God has given His command. Jonah has disobeyed. Now Jonah must sit back and suffer the consequences as God now intervenes supernaturally to alter the story. This point is made very clear by the contrast between the first two words of verse three ("But Jonah") and the first three words of verse four ("But the Lord" KJV). It is true that Jonah has rejected God. He has voiced his little "but," as we sometimes do. He is allowed to do it. God's sovereignty does not rule it out. But now God is about to voice His "BUT," and His "but" is more substantial than Jonah's.