Interestingly, we find that Jesus was troubled, himself, just a short while before as he spoke of Judas, who would betray him. A short time later, as he was still addressing his disciples, Jesus tells them not to be troubled!
The difference is that Jesus knew what was coming for him! The disciples had no clue. Jesus knew that he would handed over to the Roman authorities, tried, mocked, spit on, beaten, scourged, made a public spectacle, nailed to a cross and die there – in just a matter of hours.
The disciples still didn’t understand what Jesus was getting at – what he had been getting at for a long time. Jesus had said similar things many times before. He not only predicted his death, but his resurrection as well. But, his disciples never did realize what he was talking about (until after the fact).
Think about that: the disciples, who lived with Jesus for three years and spoke intimately with him often, didn’t get what he had been talking about throughout that whole time they were with him. They didn’t understand. They needed something more than what Jesus, who was God in the flesh, could give them!
When Jesus followed, “don’t be troubled” with “I will go and prepare a place for you”, Thomas responded, “[W]e don’t know where you’re going, how can we know the way?” When Jesus said, ““I am the way, and the truth, and the life. No one comes to the Father except through me”; Philip said, just “show us the Father, and it is enough for us.”
You can almost hear Jesus groan through the lines on the page: “Have I been with you so long, and you still do not know me, Philip?” “Don’t you know by now that you have seen the Father if you have seen me! Don’t you realize by now who I am!!” (paraphrasing what Jesus says at John 14:9-10).
But, how could finite beings really know and understand what Jesus was saying? How can God’s creation know the mind of God? We see the same kind of “exasperation” (if God can be exasperated) when God appears to Job after Job and his friends were speculating, arguing, over why Job was going through the fate that he suffered, though he insisted he was an upright man. He starts His diatribe:
“Who is this that darkens counsel by words without knowledge? …. Where were you when I laid the foundation of the earth? Tell me, if you have understanding.
The answer, of course, is that Job wasn’t there. He doesn’t know. He doesn’t understand. How could he?!
How could anyone know the mind of God unless God reveals Himself to us? How could we understand unless God reveals it to us?
How can we even be sure that we understand when God reveals something to us? The disciples didn’t even understand after spending so much time, one on one, with God in the flesh. How can earthen vessels contain spiritual things?
Jesus provides us the answer!
“If you love me, you will keep my commandments. And I will ask the Father, and he will give you another Helper, to be with you forever, even the Spirit of truth, whom the world cannot receive, because it neither sees him nor knows him. You know him, for he dwells with you and will be in you.”
It isn’t enough for us to walk with Jesus side by side and face to face. We still could not know what Jesus knows or understand what Jesus understands. But if God could dwell within us, within the temple of our hearts, minds, and souls, we could “know”, in some way – to the extent a finite mind can “know” the infinite mind of God – what God knows and understand.
Jesus knew he was leaving them, and knew he had to leave them, but he knew he wasn’t leaving them to their own devices:
“Because I live, you also will live. In that day you will know that I am in my Father, and you in me, and I in you. Whoever has my commandments and keeps them, he it is who loves me. And he who loves me will be loved by my Father, and I will love him and manifest myself to him.”
The disciples didn’t understand. How could they understand? One of them asked, “[H]ow is it that you will manifest yourself to us, and not to the world?” And, Jesus clarified further:
“[I]f anyone loves me, he will keep my word, and my Father will love him, and we will come to him and make our home with him…. These things I have spoken to you while I am still with you. But the Helper, the Holy Spirit, whom the Father will send in my name, he will teach you all things and bring to your remembrance all that I have said to you.”
And still further:
“But when the Helper comes, whom I will send to you from the Father, the Spirit of truth, who proceeds from the Father, he will bear witness about me….”
And so today, Paul can say with confidence, “The Spirit Himself testifies with our spirit that we are God’s children”, and we can say the same thing.
If the disciples could not understand what Jesus was saying though they had walked with him for three years, how much more do we struggle with the words of Jesus without his Holy Spirit. We must be born again, born of the Spirit, to be able to see the kingdom of God. These aren’t platitudes, but reality. We need the Holy Spirit to know and understand God.
We must have the Spirit, we must be “born of the Spirit”, to know and understand anything about God. The Spirit tethers us to the truth. The Spirit guides us in God’s way. The Spirit helps us when we don’t understand in our finite, human minds. The Spirit comforts us when all seems to be lost to us.
We must continually make “room” for the Spirit in our hearts, leaning not on our own understanding, but yielding our preconceived notions, and sometimes even our doctrines, to the gentle correction of the Spirit. We have this advantage that the disciples, who walked with Jesus, did not have. The Spirit comes to dwell within us, if we love Jesus by keeping his commands.
 John 13:21-30
 John 13:36-38
 Tarássō – properly, put in motion (agitate back-and-forth, shake to-and-fro); (figuratively) setting in motion what needs to remain still (at ease); to “trouble” (“agitate”), causing inner perplexity (emotional agitation) because too stirred up inside (“upset”). Tarassō means “to cause acute emotional distress or turbulence – ‘to cause great mental distress'”.
 John 14:1
 Using the same word, tarassō, John used to describe Jesus in Chapter 13.
 “The Son of Man must suffer many things and be rejected by the elders and the chief priests and the scribes and be killed, and after three days rise again” (Mark 8:31; see also Matthew 17:22; Luke 9:22). He said, if his enemies destroyed the temple (of his body), he would build it again in three days (John 2:19; Mark 14:58; cf. Matthew 26:61). He also spoke allusively of the “sign of Jonah” – three days in the heart of the earth (Matthew 12:39; Matthew 16:4). And he hinted at it again in Matthew 21:42 – “The very stone which the builders rejected has become the head of the corner.” On top of his own witness to the coming resurrection, his accusers said that this was part of Jesus’ claim: “Sir, we remember how that impostor said, while he was still alive, ‘After three days I will rise'” (Matthew 27:63).
 John 14:2-3
 John 14:6
 John 14:8
 John 14:9
 Job 38:2, 4
 John 14:15-17
 John 14:19-21
 John 14:22
 John 14:23, 25-26
 John 15:26
 Romans 8:16
 John 3:5