"We are speaking of God; what marvel if thou do not comprehend? For if thou comprehend, (God) is not God" - St. Augustine of Hippo.

So, the disciples did not comprehend. It was incomprehensible to them that God so loved humankind he would send His Son to be as one of them and to die on the cross for them. The depths of God's love, the wonder of His plans for them, were beyond their ken.

They were convinced the Messiah would be a glorious, conquering king, and they were taken up with the expectation of Elijah's return as a precursor of the Messiah. Elijah's prophetic life and actions had been aimed at restoring their faithfulness to God. Ben Sirach describes, in our First Reading of today, the Elijah they knew and waited for. The powers Jesus revealed led them to think He was Elijah come back. Jesus had to remind them that John the Baptist was like Elijah in his purifying crusade to prepare the people for the coming of the Messiah. If at all Elijah had come back, it was as John the Baptist and they should heed him as the precursor of the Messiah.

Jesus warned them that the Messiah was not coming as a political figure or a conquering king, but as a suffering Messiah. He tried to prepare them for His ultimate fate, His death on the cross. This was difficult for them to comprehend and accept.