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Jesus's Prayer We Often Doubt God Answered

Dec 17, 2023


Pastor Peder Kling


Sermon Passage: John 17:20-26

Audio Only (with the Old Testament Scripture Reading)

The Denominations Dilemma

How many Christian denominations are there in the world today? If you tried to answer that, I’d venture to say you’re wrong. Honestly, I don’t think anybody knows for sure. That’s how messy and (might I say) divided the global church has become over the last 2000 years of tradition and opinions and debates. Some say it was the protestants fault. “We were one, holy, catholic and apostolic church until Luther came around and protested, breaking away from the catholic church, making his own denomination, and starting this whole denominational thing we see today”. Some people say that. I think it’s silly. There have always been disagreements and factions in the church, since the early years of the church’s existence. Remember how Paul talked about this in his letter to the Corinthian church, who was experiencing factions over disagreements? ““I follow Paul,” or “I follow Apollos,” or “I follow Cephas,” or “I follow Christ.” Paul even says later in 1 Corinthians 3:4 “ are you not being merely human”, when you say “I follow Apollos” or “Cephas”?


Are you not being human in having an opinion, a spiritual father who you respect, that might even cause some rifts or groups within the church? We’re humans, folks. We’re not all-knowing. We don’t have perfect knowledge that would unite us. We have opinions, we’re supposed to have opinions as we pursue the truth in Jesus and in his word. Even before Martin Luther and the protestant movement, you can trace all kinds of traditions and “denominations” (broadly defined) throughout the church. 


So, is the church “one”? Is the church united? What did Jesus pray for in this prayer, we just read? Jesus says “[I ask] that they may all be one” (verse 21), “that they may become perfectly one (verse 23). Jesus is praying that the church would be “one”, unified—even unified in God’s love. In fact, in verse 21 and 23, Jesus expressly asks that this unity among believers would serve as an evangelistic witness to the world. It’d be a visible, observable unity that draws people to the faith!


Did God answer this prayer? How do we think about this passage, folks? It’s a shocking passage, and I think we’re often tempted to think it’s not a prayer request God answered—perhaps he hasn’t answered it yet. Perhaps we look at the denominations and traditions throughout the world today and say “I doubt God will ever answer this one. At least, not until Jesus’s second coming and we’re all in glory.” Ever think that way about this passage? 


Correcting Misunderstandings

Folks, as we walk through this passage, I want to correct that misunderstanding—and perhaps other misunderstandings that often relate to this passage. I believe this prayer request, folks, was answered and is being answered to this day, and that there is much comfort and hope for us in this prayer request this morning. 


So yes, we’re going to consider the various requests Jesus makes in this prayer, and especially we’ll consider some common ways this prayer is misunderstood. Then, as we clarify the misunderstandings, I think we’ll see how this prayer has been and is being answered by the Father to this day. So, let’s look for the misunderstandings, and find some clarity in Jesus’s prayer for us, for our encouragement.


Misunderstanding #1: Who Is Jesus Praying For?

Let’s begin with the first verse of our passage. Look with me at verse 20. 


“I do not ask for these only, but also for those who will believe in me through their word…


Who is Jesus referring to, in this? He’s obviously identifying the people he’s praying for. Who is he identifying? “Not… these only, but also for those who will believe in me through their word.” 


Obviously first, Jesus is identifying his 11 disciples, who he mentioned earlier in the prayer. That’s who Jesus is referring to when he says “I do not ask for these only”—that is, his 11 disciples. You may remember some direct references to the 11 disciples in last week’s passage, if you look back at verse 12. Jesus says, 


[Father,] while I was with them, I kept them in your name, which you have given me. I have guarded them [I kept them… I have guarded them], and not one of them has been lost except the son of destruction, that the Scripture might be fulfilled. 13 But now I am coming to you, and these things I speak in the world, that they may have my joy fulfilled in themselves.


So Jesus is making an obvious reference to his disciples there—whom he didn’t lose while he was with them, except for the son of destruction whom he was supposed to lose. He’s praying for their protection, their perseverance. In verse 15, he’ll ask that the Father not take them out of the world but keep them in the world, even as the Father would keep or protect them in his name and salvation. 


So, there are clear references to the 12 disciples, there in verse 12. Although, is he only praying for the 11 disciples in this prayer—perhaps, even, in that part of the prayer we looked at last week? Is he only praying for his 11 disciples in that first part of the prayer, and now in our passage, in verse 20, he begins to pray for (quote) “those who will believe in me through their word”? 


I think that’s how we might be tempted to read this, and this is getting at our first common point of confusion over this passage. While certainly Jesus does single out his disciples in verse 12, and perhaps have them in immediately mind in other ways in verses 6–8, I have every reason to believe that when Jesus is praying for the unity and protection and consecration of his disciples in the first half of this prayer, he’s not merely thinking of his 11 disciples. 


As prays that his 11 disciples would be sanctified in truth (say, in verse 17), he’s praying the church would be sanctified in truth. As he’s praying that his 11 disciples would be preserved and kept by the Father, he’s praying the same for all his disciples. He even says, generically, “I am not praying for the world but [perhaps, generically] for those whom you have given me” (verse 9), and then verse 11, “Holy Father, keep them in your name.”  This is a prayer for the church, for you and me, even as we’d be founded upon the ministry and witness of the apostles. We believe upon the apostles’ foundation—upon their word as Jesus moved them to write scriptures. Although, in praying for his apostles, Jesus is praying for all of his disciples.


People will say “Jesus prays for his 11 disciples in verses 6–19, and then he prays for the rest of the church in verses 20–26 (our passage, for this morning)”. I don’t think it’s that clear-cut, black and white. Jesus had your protection, perseverance, and sanctity in the truth in mind when he prayed those words, earlier in last weeks’ passage. Hence, our passage this morning begins not by saying “and now I pray for those who would believe in me through the disciples’ witness.” He doesn’t make an immediate, clear “I was praying for them, and now I’m praying for the rest of the church.” What does he say? Again, verse 20—


I do not ask for these only, but also for those who will believe in me through their word…


He’s saying, “In what I’m praying, in what I’ve said, I’m not only asking in reference to these disciples, but also for the rest as well.” He’s clarifying, doubling down on identifying this prayer for his disciples as a prayer for his disciples (period). 


One man points out that the verb tense in verse 20 really emphasizes this. It’s a present active indicative verb, to say “presently, now, I am not asking for them alone, but presently, now, I am asking also for those who would believe through their word”—and what does he bring up? He brings up many of the same things he already prayed for earlier—the unity and perseverance and love of his disciples. Jesus is going out of his way, in this passage, to say “the things I’ve prayed for, perhaps immediately in reference to my 11 disciples, I’m not only praying that for them but I’m praying the same even for all those who will come after them.” 


In other words, Jesus is going out of his way to make clear that he is indeed—even in what he has prayed—he really is praying for you. “This isn’t just a prayer for my 11 disciples, O Father. No. I have a bigger, broader vision in mind. I have a bigger people in mind. I’m praying the same for all of them too—for their unity and perseverance and protection and love and fellowship in God.” 


Sometimes I hear some of you pray this way in Wednesday night prayer and Bible study, or during other occasions of prayer in the life of our church. We do this often. “Lord, I pray for Brad and Carol, for Cindy, for Roshan and Tazeena. They’ve really been hit hard by the sicknesses of this flu and cold season. Protect them, keep them in the faith—and I’m not praying just for them, O Father, but I’m praying the same for all at Covenant. Keep us healthy. Keep us all steady in the faith. Keep our unity abounding in Christ, in the Father, loving and serving one another so that our neighborhood would see in us the love of Christ.” Isn’t that how we pray? We’ll often start a prayer in reference to an immediate need, but then broaden the same prayer request to a bigger group of people, a bigger cause, a bigger need. Jesus prayed that way—with you and me in mind. 


And guess what? The church is still here, professing and confessing the same apostolic faith that the church confessed 2000 years ago. We can talk about denominations (and all that) in a moment, but it’s certainly true, folks. The fact that there is still an obvious referent to Jesus’s prayer (a people whom his prayer can be applied to) 2000 years after the fact is astonishing. “I do not ask for these only, but also for those who will believe in me through their word, that they’d be united and preserved in the Father’s love and protection.” Just think—there are still people who are believing in Jesus “through their word”—through the apostles’ word—2,000 years later. I think that’s just a hint at where this is going. It’s a hint at just maybe God has answered Jesus’s prayer in one way or another.


So, there’s one misconception to clear up. We cannot make a rigid outline of Jesus’s prayer, here, and say that Jesus is only praying for his 11 disciples in verses 6–19, and he’s only praying for the rest of us in verses 20–26. There’s some overlap, here. “I’m not only praying for the 11, but everyone else as well…”. Jesus is overflowing with love and concern for all his disciples in this prayer—for their protection, perseverance, sanctity in truth, unity, love, and fellowship with the Father. He wants that for us. He’s prayed for it. He died for it. 


And really (just to insert a quick reminder of the context of this prayer)—hear that. Jesus prayed for it, and then he died for it. This is his prayer for us in the moments before he goes to the cross. When we pray for God’s protection and blessing and love and help in a hard moment, whose sacrifice for sin do we appeal to for confidence that God hears us and might bless us? We appeal to Jesus’s sacrifice, his blood. I often think of prayers as a blood-bought privilege. Folks, Jesus is praying for us as our priest—God in the flesh, the perfect mediator—and then he’s going to go to the cross in order to ensure his prayers are heard and accepted before the Father. Nobody in the history of the world has ever prayed like that, except Jesus. “I pray for them on the basis of my righteousness and my sacrifice which I’m about to go make on their behalf, that you might bless them O Holy Father.” We cannot forget the context of this prayer, folks. It’s not just a prayer for his 11, or just a prayer for all his disciples. It’s a prayer that he prayed and then he secured through his own sacrifice only hours later. Remember Hebrews 7?


5 Consequently [because of his one sacrifice and his resurrection to eternal glory], he is able to save to the uttermost those who draw near to God through him, since he always lives to make intercession for them.


He prayed for all his people. He died and rose for them. He’s still praying, still interceding, always with his people in mind.


Misunderstanding #2: The Problem of Unity

Let’s keep reading in our passage, to find more clarity and encouragement in this passage. Verse 20, now going into verse 21—


20   “I do not ask for these only, but also for those who will believe in me through their word, 21 that they may all be one, just as you, Father, are in me, and I in you, that they also may be in us, so that the world may believe that you have sent me.


So, Jesus is praying “not only” for the eleven, “but also” for everyone who will eventually believe (the whole church)—“that they all may be one.” He’s praying for the church’s unity—and, not just any unity. He’s praying for the church’s unity (or even union) with God himself. “That they all [the eleven disciples with everyone else] would be one, just as you, Father, are in me and I in you.” So this is a union kind of unity. This isn’t a unity in some kind of club or external organization. We’re talking about “I in you and you in me” unity (or union). 


What on earth is Jesus referring to, here? I’ve heard people use this passage to do really weird stuff, folks—to imply that somehow we are made to be God or made to be small-g gods, or something like that. People love to get all esoteric or philosophical about this verse. Is that what Jesus is referring to, here? Are we somehow brought into the infinite, perfect union of the Trinity?


Honestly, it’s a mystery. In many ways, our union with God is a mystery that’s rooted in the mystery of the incarnation of Jesus, the Son of God, taking on flesh. I mean, think about it. How can we even begin to talk about humans being united—made one—with God in any sense of the term at all? How can we begin to talk about that? The incarnation, folks—the Christmas story. God united himself with us. God took on our flesh, defeated sin and the curse in the flesh, in order that in the flesh we might be brought up together in Christ to God through the eternal Son of God in our flesh. Our union with God in this passage is rooted in Jesus being our priest, is rooted in the Son of God taking on our flesh, and I think we’re diving into mysteries that we cannot even begin to fathom or comprehend. As Winston Churchill famously coined the term, “It's a riddle wrapped in a mystery inside an enigma.” 


But, it’s not incomprehensible. It’s not without meaning, or purpose, or glory, even for us insofar as we can understand it. Certainly, Jesus is not saying that we are being made to be God in our union with him. There is only one God, there will always and ever be only one God, the Triune God for all eternity. Through Jesus, we’re brought up into that glory, that life, that blessing. That seems to be what Jesus is saying in the next verse, isn’t it? Verse 22, as he continues to define this for us—


The glory that you have given me [as the eternal Son of God, in the flesh, bearing the office of the Messiah] I have given [that] to them, that they may be one even as we are one


It’s really our only hope, isn’t it? His life, his glory is our only hope. It’s the only way, if we truly understand the depravity and sin and curse we’re stuck before God. Jesus has received and given—or perhaps manifested—God’s glory in the flesh so that we might see it by faith, receive it, and so be united in it. Of course, by his “glory”, we’re referring to God’s character and his blessings of grace, peace, joy, kindness, forgiveness, righteousness, eternal life. Jesus didn’t just manifest it, but he gave it—he gave God—to us, that we might be so united.


Understand the desperation in this, folks. Outside of God’s life, we’re left to our lives which are cursed and destined to death. Without being united to God’s eternal life and righteousness, we’re left to our life and righteousness. Without being united into God’s love, we’re left to our fallen and sinful loving that fall so short of God’s glory. God had to be the answer. He gave us the answer in Jesus, God in the flesh, intent to bring us in the flesh to God.


[Father… I pray] that they may all be one, just as you, Father, are in me, and I in you, that they also may be in us… 


If we aren’t united in God, and in the Father, what are we united under? Our common earthly Father Adam, in whom “all die”? Or perhaps we can be united in worldly, fleeting things like football or Shakespeare or small talks about the weather, or politics or our jobs. There’s lots of hope and glory given in those things, aren’t there? 


Jesus gave us God. He gave us God’s glory, that we might be one—united literally “in us”, the Sons says to the Father. It’s mysterious, but unfathomably glorious and filled with hope and peace for us this morning.


Now just for clarity, to be sure, let’s parse out the comparison Jesus makes, there—really press into it. Jesus prays that we would be one “just as you, Father, are in me and I am in you”. I think it’s worth pressing into that comparison a little bit, because it is the comparison that especially gets us scratching our heads. Jesus is one in the Father as God, in Trinitarian union. That’s the comparison Jesus is making—that we’d be one just like that. How can we make sure we don’t take that too far, and make ourselves into additional persons of the Trinity, or something weird like that? 


One commentator stated it this way, referring to how Jesus spoke of his union with the Father in other parts of John’s gospel. He says, in John’s gospel, “the Father is actually in the Son, so much so that we can be told that it is the Father who is performing the Son’s works (14:10); yet the Son is in the Father, not only in dependence upon and obedience to him, but [the Son is] his agent in creation (1:2-3) and his wholly concurring Son in the redemption and preservation of those the Father has given them.”


In other words, throughout John’s gospel, Jesus as God-in-the-flesh, as the Messiah, speaks of his union with the Father in terms of love, in terms of obedience, in terms of taking part in God’s greater mission. It’s a perfect union of love and purpose—when the Son acts, it’s as though the Father is acting (14:10), and when the Father purposes, the Son obeys with full dependence upon the Father for strength and wisdom and help. That’s how John’s gospel often speaks of the Father’s unity with the Son, and I think that’s helpful to see.


So, there’s where all the unity sits for us. Remember, Jesus came to unite himself with us in the flesh—to unite God with us in the flesh. By faith, we’re united with him—in his purpose, in his love, in his obedience and righteousness, in his actions. When the apostles spread he kingdom in Acts, it was regarded as Jesus himself continuing his work through the apostles. The apostles were serving, so Jesus was serving through them, and so the Father was serving through the Son and the son’s people. It’s unity, folks, hinging on the Son of God who took on our flesh for our union with the Father’s love and purpose and strength and fellowship and glory. It’s an amazing thing. 


[Father… I pray] that they may all be one, just as you, Father, are in me, and I in you, that they also may be in us… 


Later in this prayer, Jesus will only provide more clarity on all this. In verse 23, again, he’ll pray for perfect unity. Verse 23, “I in them and you in me, that they may become perfectly one…”. As we would get into verses 24–26, we find that unity described in terms of fellowship with the father. It’s not abstract, impersonal, esoteric unity. It’s personal unity—fellowship and love. Verse 24—


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


Or verse 26, saying something very similar and all the more glorious—


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 in them, and I in them.”


It’s unity, folks—union with the Son in the Father, and it’s all of our unity, together, with the whole church. It’s a unity in God’s resolve, his purpose, his love, his forgiveness, his fellowship—and yes, in his Son who took on our flesh. 


Jesus prayed for it. He took on our flesh for it, he prayed for it, he died for it, he rose for it, and the Father has blessed it all. 


So, hopefully that clarifies a few misunderstandings surrounding this passage. No, Jesus is not praying that we would be god, or become god in any way. And no, Jesus is not praying that the church would create its own unity through uniting around its own creeds and confessions. Ultimately, Jesus is praying that his people would be united with the Father and with one another insofar as they are united together in him, by faith, through the cross. This is something Jesus has accomplished and prayed for, and that the Father ultimately blessed. It’s not something we do as a universal church by creating creeds and confessions for us to unite around through some confessional or denominational unity. This is spiritual, blood-bought unity which we are first called to receive by faith, and then pursue together as we pursue Jesus, and all truth in Jesus. 


But, what of denominations? We should be grieved by them, no? We should pray for the unity of the church. Paul even commands us to it in Philippians 2, where he actually tells us “complete my joy by being of the same mind, having the same love, being in full accord and of one mind.” He’s not just saying “agree on the essentials”. Paul is commending us to really pursue deep unity in deep truths in Jesus. We ought to pursue that unity, even with other denominations. We ought to have an ecumenical flavor to us, and yet we ought to do it honestly with a desire for truth and obedience to Christ. We ought to do it recognizing that our unity is not ultimately something we do in uniting as denominations, and such. Our unity is something God has done in Jesus, and it’s a unity with one another in God. It’s a unity of truth, purpose, love, and fellowship in God, in Jesus. 


So yes, be grieved by the divisions within the greater church, but we need not be distraught over them. Jesus has given us perfect, substantial unity in him, with the Father, folks. Insofar as there is disagreements among brethren that might even form denominations, I think it is telling that I can enjoy a profoundly different fellowship and unity with a Baptist or Methodist or Anglican Christian who loves Jesus than I can with someone who isn’t a Christian at all. The Lord often uses men and women from other denominations to convict me of sin, teach me about Jesus, encourage and strengthen me in the faith, motivate me to obedience and to be involved in Christ’s kingdom on earth. There’s unity there, isn’t there? 


As one minister said, “this prayer isn’t a command”. It’s not a command—“be unified, church!”. It’s a prayer, folks—Jesus’s prayer, and that should say something about our unity. If Jesus’s prayers are answered on the basis of our righteousness, his prayers won’t be answered. If his prayers are answered on the basis of his work on the cross, and the Father’s blessing, then I think we should listen in and learn something, and be encouraged, and be friendly—with Christian love—with those who profess Jesus faithfully. We are united with them, folks. “What God has united, let not man separate.” Denominations don’t separate that, folks.


So, you might say we’ve address three misunderstandings about this passage so far. (1) This prayer—all of it (not just the last few verses)—is Jesus’s prayer for all his disciples’ unity and perseverance in the faith; (2) Jesus is praying not that we would be united with God and so be God in some weird esoteric way to make us divine, but that we’d be united with God as Jesus our human mediator is united with God, united in his love and fellowship and mission. Then (3) this is indeed a prayer, not a command—it’s Jesus’s prayer for our unity in him, in the Father, based on what he ultimately accomplished for us.


Misconception #3: Getting Rid of Denominations Is Our Hope for Christian Witness

Now, there’s one more misconception in this passage. There’s something Jesus repeats twice in this passage. I mentioned it before, but we haven’t elaborated on it. Look at the repetition in verses 21 and 23. Verse 21, Jesus prays we’d be one “so that the world may believe that you have sent me”. Then verse 23, he prays “that they may become perfectly one, so that the world may know that you sent me.” See the repetition there? 


Our unity, Jesus prays, is intended “so that the world may know you sent me”—that is, so the world will know Jesus is the Savior, God in the flesh, from the Father. Our unity serves our witness. There’s no debating that. So many people either leave the faith or are further embittered against the church when they hear that Christians aren’t acting like Christians—when they are dividing churches and bickering and hating one another. 


On the other hand, yes, Christian unity helps Christian witness. 


However, I think we need to be careful. We need to root ourselves rightly, folks. Our union with whom helps Christian witness? Yes, in a secondary sense, our union with one another helps. But consider what Jesus is emphasizing in verses 21 and 23. 


that they also may be [one] in us, so that the world may believe that you have sent me… (verse 21)


I in them and you in me, that they may become perfectly one, so that the world may know that you sent me… (verse 23)


What union is Jesus ultimately emphasizing, here, as having the most power in our witness to the world? He’s speaking ultimately about our union with him, with God. Nobody is going to know Jesus through us if we’re not united to God in Jesus. Our union with God—and then with one another—is what matters. 


There may be a temptation for us to think, “getting rid of denominations is our hope for Christian witness to the world”. That’s not our hope, folks. Our hope is having true Christian unity with God and with one another, by faith, and perhaps even letting that unity in Christ rather than denominations overcome our denominational differences whenever possible. That’s our hope, folks—union with God and his Son Jesus Christ, who took on our flesh so that we might enjoy union with God in all his glory and blessings and mission to the world. That’s the foundation which will effect real and powerful witness to the world.



So, brothers and sisters, Jesus is praying for you. He did pray for you—for your protection, perseverance in the faith, for your union with God and our union with one another. He secured it all at the cross. That’s our hope, folks. Seek unity with one another, and with other believers of different denominations, and do it by seeking Jesus. He took on our flesh for it, folks. Enjoy the fellowship, and enjoy it heartily.

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