While I was with them, I protected them and kept them safe by that name you gave me. None has been lost except the one doomed to destruction so that Scripture would be fulfilled.
Jesus had kept the disciples by the name of God; He had protected them by the power of the God who revealed Himself through Jesus (6:39). There was just one unfortunate exception (Mark 14:21).
John 6:39 And this is the will of him who sent me, that I shall lose none of all that he has given me, but raise them up at the last day.
Mark 14:21 The Son of Man will go just as it is written about him. But woe to that man who betrays the Son of Man! It would be better for him if he had not been born.”
“the one doomed to destruction” is Judas, of course. There is a wordplay in the Greek which we miss in our English. Phillips tries with “not one of them was destroyed, except the son of destruction” and NEB tries with “not one of them was lost except the man who must be lost.” “The one doomed to destruction” (NIV) = “the son of perdition” (KJV) points to the character and not the destiny of Judas. Judas is here characterized by his lostness, and is not referred to as being predestined to be lost. Calvin notes that “It would be wrong for anyone to infer from this that Judas’ fall should be imputed to God rather than to himself, in that necessity was laid on him by the prophecy.” Judas had free will and made wrong choices for which he had to pay. However, God used his evil act to bring about His own purposes. There is a combination of divine and human actions in this, but this passage stresses the divine side. It was God’s will for Jesus to be handed over to His enemies to be crucified. God knows everything, even the future. He knows every action we will ever take (and yet He still loves us!) He knew beforehand what Judas would do and made His prophecies accordingly. Morris notes that “The Father’s will was done, both in the eleven and in the one, for scripture was fulfilled.” The scripture here referred to is probably (Psa 41:9).
Psalms 41:9 Even my close friend, whom I trusted, he who shared my bread, has lifted up his heel against me.
As Jesus kept His disciples, so shall He keep us. The fact that He will keep us implies that we are weak and in need of His protection and provision. It also implies that we are valuable to God and worth keeping. Jesus is very good at taking care of His own (John 10:14-16).
John 10:14-16 “I am the good shepherd; I know my sheep and my sheep know me— just as the Father knows me and I know the Father—and I lay down my life for the sheep. I have other sheep that are not of this sheep pen. I must bring them also. They too will listen to my voice, and there shall be one flock and one shepherd.