9 “You shall seek me, and shall not find me: and where I am, there ye cannot come.” Here He has already foretold His resurrection; for they would not acknowledge Him when present, and afterwards they sought Him when they saw the multitude already believing on Him. For great signs were wrought, even when the Lord was risen again and ascended into heaven. Then mighty deeds were done by His disciples, but He wrought by them as He wrought by Himself: since, indeed, He had said to them, “Without me you can do nothing.” When that lame man who sat at the gate rose up at Peter's voice, and walked on his feet, so that men marvelled, Peter spoke to them to this effect, that it was not by his own power that he did this, but in the virtue of Him whom they slew. Many pricked in the heart said, “What shall we do?”
For they saw themselves bound by an immense crime of impiety, since they slew Him whom they ought to have revered and worshipped; and this crime they thought inexpiable. A great wickedness indeed it was, the thought of which might make them despair; yet it did not behoove them to despair, for whom the Lord, as He hung on the cross, deigned to pray. For He had said, “Father, forgive them; for they know not what they do.” He saw some who were His own among many who were aliens; for these He sought pardon, from whom at the time He was still receiving injury.
He regarded not that He was being put to death by them, but only that He was dying for them. It was a great thing that was forgiven them, it was a great thing that was done by them and for them, so that no man should despair of the forgiveness of his sin when they who slew Christ obtained pardon. Christ died for us, but surely He was not put to death by us? But those men indeed saw Christ dying by their own villany; and yet they believed on Christ pardoning their villanies. Until they drank the blood they had shed, they despaired of their own salvation.
Therefore said He this: “You shall seek me, and shall not find me: and where I am, you cannot come;” because they were to seek Him after the resurrection, being pricked in their heart with remorse. Nor did He say “where I will be,” but “where I am.” For Christ was always in that place whither He was about to return; for He came in such manner that He did not depart from that place. Hence He says in another place, “No man has ascended into heaven, but He who came down from heaven, the Son of man who is in heaven.” He said not, who was in heaven.
He spoke on the earth, and declared that He was at the same time in heaven. He came in such wise that He departed not thence; and He so returned as not to abandon us. What do ye marvel at? This is God's doing. For man, as regards his body, is in a place, and departs from a place; and when he comes to another place, he will not be in that place whence he came: but God fills all things, and is all everywhere; He is not held in places according to space. Nevertheless the Lord Christ was, as regards His visible flesh, on the earth: as regards His invisible majesty, He was in heaven and on earth; and therefore He says, “Where I am, there ye cannot come.”
Nor did He say, “You shall not be able.” but “you are not able to come;” for at that time they were such as were not able. And that you may know that this was not said to cause despair, He said something of the same kind also to His disciples: “Whither I go ye cannot come.” Yet while praying in their behalf, He said, “Father, I will that where I am they also may be with me.” And, finally, this He expounded to Peter, and says to him, “Whither I go you can not follow me now, but you shall follow me hereafter.”
Source: Tractates on the Gospel of John (New Advent)