The disciples were trying to fit together what they had been taught with what they had just seen. The scribes taught that Elias, the Greek form of the name Elijah, must come first. Gill explains this as "before the Messiah comes, or before the setting up his kingdom in greater glory." On the mountain the disciples had seen Elias with Jesus (Mark 9:4), and they were already puzzled about Jesus' words on rising from the dead (Mark 9:10).

Writing on the parallel in Matthew 17:10, Barnes says the transfiguration had taken away their doubts that Jesus was the Messiah, but they remembered that "it was a common doctrine among the Jews that Elijah would appear before the Messiah came." In Barnes' words, their question amounted to this: "Were they right or wrong in their expectation of Elijah?"

Jesus answered directly: "Elias verily cometh first, and restoreth all things" (Mark 9:12). He then pointed them to what is also written, that the Son of man "must suffer many things, and be set at nought." Finally He told them, "Elias is indeed come, and they have done unto him whatsoever they listed, as it is written of him" (Mark 9:13). Matthew adds that the disciples then understood "that he spake unto them of John the Baptist" (Matthew 17:13).

The scribes were experts in the law of Moses who copied, taught, and explained it. Their expectation of Elijah's coming rests on the promise at the end of the Old Testament: "Behold, I will send you Elijah the prophet before the coming of the great and dreadful day of the LORD" (Malachi 4:5). Gill links the words "as it is written of him" in Mark 9:13 to this prophecy in Malachi 4:5.

Barnes explains that to "restore" means to heal, to correct, "to put in proper order." He says John the Baptist "corrected many of their notions about the Messiah" and was the instrument of a widespread reformation among the people.

This question shows that God keeps His word, though not always in the way people expect. The scribes were right that Elias must come first. Jesus said so plainly (Mark 9:12). But they missed that he had already come in John the Baptist, and that they had done to him "whatsoever they listed" (Mark 9:13). Barnes, on the parallel in Matthew 17:12, says this means they had done to John as they pleased, "that is, they had put him to death."

The disciples had just heard the Father say of Jesus, "This is my beloved Son: hear him" (Mark 9:7). Their question shows them doing exactly that: bringing a hard question to Jesus and listening to His answer. He did not throw out the Scriptures behind the scribes' teaching. He opened them more fully.