Jesus wanted the disciples to hold two things together: the glory they had just seen and the suffering that was coming. He agreed that Elias "verily cometh first, and restoreth all things." Then He pointed them to another part of Scripture the scribes were not stressing: what "is written of the Son of man."

Matthew Henry puts it this way: "it is also prophesied of the Son of man, that he must suffer many things, and be set at nought... and though the scribes do not tell you so, the scriptures do." Jesus had already said plainly that the Son of man "must suffer many things" (Mark 8:31), and Peter had rebuked Him for it (Mark 8:32). Gill says that John, the Elias who came first, restored all things partly by giving "the true sense of such passages of the sacred writings, which related to the contemptuous usage, rejection, and sufferings of the Messiah."

Jesus continues in the next breath: "But I say unto you, That Elias is indeed come, and they have done unto him whatsoever they listed, as it is written of him" (Mark 9:13). What was done to the forerunner pointed to what would be done to the Son of man. Matthew records Jesus saying it outright: "Likewise shall also the Son of man suffer of them" (Matthew 17:12). Yet when Jesus taught again that He would be killed and rise the third day, "they understood not that saying, and were afraid to ask him" (Mark 9:31-32).

In the KJV this sentence ends with a period, following the Textus Receptus, the Greek text behind the KJV. Other Greek editions, such as Nestle's, punctuate it as a question, and the ESV translates it, "And how is it written of the Son of Man...?" Either way, the clause turns on the Greek word pos, "how," and calls the disciples to think about what Scripture says.

"Set at nought" translates one Greek verb that Thayer defines as "to hold and treat as of no account, utterly to despise." Thayer notes that the Septuagint, the ancient Greek translation of the Old Testament, uses it often for Hebrew words meaning to despise or reject. Matthew Henry describes the Son of man as one who "must be a reproach of men, and despised of the people," words taken from Psalm 22:6.

This question reveals something about God's plan: suffering came before glory, and it was written beforehand. The disciples had just seen Jesus shining on the mountain. Jesus turned them from that glory to what was written of His suffering. Both Elias' coming and the Son of man's suffering were "written" (Mark 9:12-13). God's plan was not failing when the Messiah was despised. It was being fulfilled.

Gill sees the meaning of that suffering. He calls the Son of man "the Lamb of God typified in the sacrifices of the law, who by his sufferings and death takes away the sin of the world." The One who would be set at nought was the One the Father had just called "my beloved Son" (Mark 9:7).