The price that John the Baptist would pay for his prophetic message was his life. He had spoken the word of the Lord without fear. Herod Antipas of Galilee threw John in prison at the fortress of Machaerus because John had publicly rebuked Herod for marrying his brother's wife.
For the moment, John was in prison. Jail cells in those days were terrible places: dark, damp, and infested with rats. When an individual was thrown into prison, he or she was awaiting two things: trial or execution.
It should not be surprising that under these conditions, John would begin to have his doubts about Jesus' Messiahship. John's disciples have been reporting to him Jesus' comings and goings. It could have been that John's dire situation in prison and the reports of John's disciples that Jesus was not acting in conventional and acceptable messianic fashion, led John to doubt Jesus' calling as the Anointed One.
Jesus was not living up to the expectations of the people. The people of Israel wanted a Messiah to bring in God's Kingdom that would give them power and control over the pagans. They wanted Jesus to lead a messianic revolt, to take up the sword and overthrow the Romans tossing Pilate out of Judea. Perhaps this is what John wanted as well. Just because John believed Jesus to be the Messiah, did not mean he understood how Jesus would fulfill that messiahship.
Some have suggested that John's question was not asked for his own sake, but for the sake of his disciples. Some believe that this was an attempt by John to show his disciples that Jesus truly was the Messiah; but no such insulation of John's faith is necessary. There is no danger to John's character because of his doubt. Faith is fashioned in the workshop of doubt. Jesus will point out that John remains a great man for good reason.
"Are you the one who was to come, or should we expect someone else?" Notice that Jesus does not answer the question directly. He tells John to judge for himself: "Go back and report to John what you hear and see: the blind receive sight, the lame walk, those who have leprosy are cured, the deaf hear, the dead are raised, and the good news is preached to the poor."
Jesus appeals to the evidence. Jesus himself affirms the discipline of apologetics. Apologetics has fallen on hard times in certain Christian post-modern circles, where reason is denigrated in favor of experience (often referred to as relationship) as if the two can be separated so neatly. While it is true that certain apologetical methodologies lean too closely toward rationalism, here we see in this passage from Matthew, the importance Jesus places on the appeal to reason and experience.
The question is asked today, "Is Jesus the one?" The only answer worth considering is, "Look at the evidence. what do you see, what do you hear?" The only way others will know that Jesus is the one is by looking at the character, worship, ministry, and scholarship of his disciples. Will the evidence we produce assist others in considering Jesus? Are we living up to the expectations of the Messiah we follow?
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I do not seek to understand that I may believe, but I believe in order to understand. For this also I believe, –that unless I believed, I should not understand.-- St. Anselm of Canterbury (1033-1109)