Why John is often misunderstood is because the Greek word "en" is often incorrectly translated.

When used in the sense of “in God,” or “in Christ,” the word “in” refers to a close communion, a tight fellowship. It was part of the covenant language of the day, when people spoke of being either “in” or “cut off from” the covenant.

-- Morgridge, pp. 116 and 117
-- Racovian Catechism, pp. 142 and 143
-- Spirit & Truth Fellowship International

The reason why this is important, is because the laws of physicals does not allow Jesus to be "in" someone, unless Jesus is a spirit or a divine being, which supports the Trinitarians' view.

However, as seen above the Greek word "en" could also mean "by" or "with", for example:

After his mother Mary was betrothed to Joseph, before they came together, she was found with (ἐν) child of the Holy Spirit. -- Matthew 1:18 (NKJV)

“Behold, the virgin shall be with (ἐν) child, and bear a Son, and they shall call His name Immanuel,” -- Matthew 1:23 (NKJV)

“But you, Bethlehem, in the land of Judah, are not the least among (ἐν) the rulers of Judah” -- Matthew 2:6 (NKJV)

And Jesus went about all Galilee, teaching in their synagogues, preaching the gospel of the kingdom, and healing all kinds of sickness and all kinds of disease among (ἐν) the people. -- Matthew 4:23 (NKJV)

But I say to you, do not swear at all: neither by (ἐν) heaven, for it is God’s throne; nor by (ἐν) the earth, for it is His footstool; nor by (ἐν) Jerusalem, for it is the city of the great King. -- Matthew 5:34-35 (NKJV)

... and so forth.

It radically changes the meaning of John 13 to 17 when we consider the original meaning of the Greek word "en":

Then Jesus provide analogies to explain what he just taught:

I am the true vine (vine of truth) and my Father is the vinedresser (farmer).

Every branch in me that does not bear fruit He takes away;
and every branch that bears fruit He prunes (cleanse/purify), that it may bear more fruit. You are already clean because of the word which I have spoken to you.

Abide (stay/endure) with me, and I with you. As the branch cannot bear fruit of itself, unless it abide (stay/endure) in (with) the vine, neither can you, unless you abide (stay/endure) with me.

I am the vine, you are the branches. He who Abide (stay/endure) with me, and I with him, bears much fruit;
for without me you can do nothing. If anyone does not abide (stay/endure) with me, he is cast out as a branch and is withered; and they gather them and throw them into the fire, and they are burned.

If you abide (stay/endure) with me, and my words abide (stay/endure) with you, you will ask what you desire, and it shall be done for you. By this my Father is glorified, that you bear much fruit; so you will be my disciples.

-- John 15:1-8 (NKJV but ἐν restored)

To summarize:

(Note that the Holy Spirit is not mentioned as a separate member of the Godhead in Jesus' analogy)

Then Jesus summarizes what he meant with his analogy:

“As the Father loved me, I also have loved you; abide in my love. If you keep my commandments, you will abide in my love, just as I have kept my Father’s commandments and abide in His love.

These things I have spoken to you, that my joy may remain with you, and that your joy may be full.

This is my commandment, that you love one another as I have loved you.

-- John 15:9-12 (NKJV)

Then Jesus continue to explain what he means by "love":

Greater love has no one than this, than to lay down one’s life for his friends. You are my friends if you do whatever I command you. No longer do I call you servants, for a servant does not know what his master is doing; but I have called you friends, for all things that I heard from My Father I have made known to you.

You did not choose me, but I chose you and appointed you that you should go and bear fruit, and that your fruit should remain, that whatever you ask the Father in my name He may give you. These things I command you, that you love one another.

-- John 15:13-17 (NKJV)

Then Jesus contrast his disciples with the people of the world:

If the world hates you, you know that it hated me before it hated you. If you were of the world, the world would love its own. Yet because you are not of the world, but I chose you out of the world, therefore the world hates you.

Remember the word that I said to you, "A servant is not greater than his master."

If they persecuted me, they will also persecute you.
If they kept (guard/heed) my word, they will kept (guard/heed) yours also.

But all these things they will do to you for my name’s sake, because they do not know Him who sent me.

If I had not come and spoken to them, they would have no sin, but now they have no excuse for their sin.

He who hates me hates my Father also. If I had not done among them the works which no one else did, they would have no sin; but now they have seen and also hated both me and my Father. But this happened that the word might be fulfilled which is written in their law:

"They hated Me without a cause."

-- John 15:18-25 (NKJV)

The Jesus closed with:

“I still have many things to say to you, but you cannot bear them now.

However, when He, the Spirit of truth, has come, He will guide you into all truth; for He will not speak on His own authority, but whatever He hears He will speak; and He will tell you things to come. He will glorify me, for He will take of what is mine and declare it to you. All things that the Father has are mine. Therefore I said that He will take of mine and declare it to you.

A little while, and you will not see me;
and again
a little while, and you will see me, because I go to the Father.

-- John 16:12-16 (NKJV)

These words caused some confusion among the disciples:

Then some of His disciples said among themselves, “What is this that He says to us, ‘A little while, and you will not see Me; and again a little while, and you will see Me’; and, ‘because I go to the Father’?”
They said therefore, “What is this that He says, ‘A little while’? We do not know what He is saying.”

-- John 16:17-18 (NKJV)

Then Jesus explain what he meant:

Now Jesus knew that they desired to ask him, and He said to them, “Are you inquiring among yourselves about what I said, ‘A little while, and you will not see Me; and again a little while, and you will see Me’?

Most assuredly, I say to you that you will weep and lament, but the world will rejoice; and you will be sorrowful, but your sorrow will be turned into joy. A woman, when she is in labor, has sorrow because her hour has come; but as soon as she has given birth to the child, she no longer remembers the anguish, for joy that a human being has been born into the world.

Therefore you now have sorrow; but I will see you again and your heart will rejoice, and your joy no one will take from you. And in that day you will ask me nothing.

Most assuredly, I say to you, whatever you ask the Father in my name He will give you.

Until now you have asked nothing in my name. Ask, and you will receive, that your joy may be full.

These things I have spoken to you in figurative language; but the time is coming when I will no longer speak to you in figurative language, but I will tell you plainly about the Father. In that day you will ask in my name, and I do not say to you that I shall pray the Father for you;

for the Father Himself loves you, because you have loved me, and have believed that I came forth from God. I came forth from the Father and have come into the world. Again, I leave the world and go to the Father.

-- John 16:19-28 (NKJV)

Then Jesus disciples respond that they finally understood what he had meant:

His disciples said to Him, “See, now You are speaking plainly, and using no figure of speech! Now we are sure that you know all things, and have no need that anyone should question you. By this we believe that you came forth from God.”

Jesus answered them, “Do you now believe? Indeed the hour is coming, yes, has now come, that you will be scattered, each to his own, and will leave me alone. And yet I am not alone, because the Father is with me. These things I have spoken to you, that in me you may have peace. In the world you will have tribulation; but be of good cheer, I have overcome the world.”

-- John 16:29-33 (NKJV)

Then Jesus prays to his Father:

"Father, the hour has come;

• glorify Your Son that the Son may glorify You,
  • since You have given him authority over all flesh,
  • to give eternal life to all whom You have given him. And this is eternal life, that they know You, the only true God, and Jesus Christ whom You have sent.
  • I glorified You on earth, having accomplished the work that You gave me to do.
  • And now, Father, glorify me in Your own presence with the glory that I had with You before the world existed.
• I have manifested Your name to the people whom You gave me out of the world.
• Yours they were, and You gave them to me, and they have kept Your word. Now they know that everything that You have given me is from You.
• For I have given them the words that You gave me, and they have received them and have come to know in truth that
• I came from You; and they have believed that You sent me.
• I am praying for them.
• I am not praying for the world but for those whom You have given me, for they are Yours. All mine are Yours, and Yours are mine, and
• I am glorified in them.
• And I am no longer in the world, but they are in the world, and I am coming to You.
• Holy Father, keep them in Your name, which You have given me,
• that they may be one, even as we are one.
• While I was with them, I kept them in Your name, which You have given me. I have guarded them, and not one of them has been lost except the son of destruction, that the Scripture might be fulfilled.
• But now I am coming to You, and
• these things I speak in the world, that they may have my joy fulfilled in themselves.
• I have given them Your word, and
• the world has hated them because they are not of the world, just as I am not of the world. I do not ask that You take them out of the world, but that You keep them from the evil one. They are not of the world, just as I am not of the world (John 18:36).
• Sanctify them in the truth; Your word is truth.
• As You sent me into the world, so I have sent them into the world.
• And for their sake I consecrate myself, that they also may be sanctified in truth.
• I do not ask for these only, but also for those who will believe in me through their word, that they may all be one,
• just as You, Father, are with me, and I with You, that they also may be with us, so that the world may believe that You have sent me. The glory that You have given me I have given to them, that they may be one even as we are one, I in (with) them and You in (with) me, that they may become perfectly one,
• so that the world may know that You sent me and loved them even as You loved me.
• Father, I desire that they also, whom You have given me, may be with me where I am, to see my glory that You have given me
• because You loved me before the foundation of the world.
• O righteous Father, even though the world does not know You, I know You, and these know that You have sent me.
• I made known to them Your name, and I will continue to make it known,
• that the love with which You have loved me may be with them,
• and I with them.”

-- John 17:1-26 (ESV but ἐν restored)

To summarize this prayer: