Prayer Study Week 2 – Holy Spirit

Holy Spirit – Deepening of our Faith

John 3:5-8: “Jesus answered, ‘I tell you the truth, no one can enter the kingdom of God unless he is born of water and the Spirit. Flesh gives birth to flesh. But the Spirit gives birth to spirit.'”

The Example of Christ

Matthew 3:13-17: “Then Jesus came from Galilee to the Jordan to be baptized by John. But John tried to deter Him, saying, ‘I need to be baptized by You, and do You come to me?’ Jesus replied, ‘Let it be so now; it is proper for us to do this to fulfill all righteousness.’ Then John consented. As soon as Jesus was baptized, He went up out of the water. At that moment heaven was opened, and He saw the Spirit of God descending like a dove and alighting on Him. And a voice from heaven said, ‘This is my Son, Whom I love; with Him I am well pleased.’”

This story of the baptism of Jesus can be difficult for us to understand. Why did the Son of God need to be baptized with water? Why did He need to receive this anointing of the Holy Spirit? Even John the Baptist struggled to understand these things, arguing that it was him who should be baptized by Jesus.

But through this account, we begin to get an understanding of the humility of Jesus Christ, and of His conviction that all glory and wisdom was found only in His Heavenly Father. Before Jesus began any public ministry, He first willingly, humbly submitted to the outpouring of the Holy Spirit on His life, in a very public experience at His baptism.

It is important also to note that immediately following the glorious experience of His baptism, we see in Matthew 4 that the very next place to which the Holy Spirit led Jesus Christ was into the desert, into a time of trial and temptation. Before leading Him into any kind of public ministry, the Holy Spirit saw it necessary for Jesus to face His own temptations as a man, and to firmly establish His identity as the Son of God.

As we read in Matthew 4:11, Jesus Christ walked out of the desert in freedom and victory. His obedience and submission to the guidance of the Holy Spirit in these early days of His public life resulted in clear evidence of two things:

1 – His complete faith in and submission to the empowering work of the Holy Spirit.

2 – The unfailing power of the Holy Spirit to defeat the enemy. (Discussed further in section entitled “Spiritual Warfare”.)

As followers of Jesus Christ, we must begin where He began on that day in the Jordan river – in humility and submission, waiting prayerfully for the indwelling, the refining, and the empowering of the Holy Spirit in our lives. Nothing we do in His name should precede this.

Why do we need the Holy Spirit?

In Luke 22:31-34, we have the story of an account between Simon Peter and Jesus, which took place during the Last Supper, just a few hours before Jesus was arrested.

As Jesus was talking with the disciples, at one point He turned and addressed Simon Peter directly, saying, “Simon, Simon, Satan has asked to sift you as wheat. But I have prayed for you, Simon, that your faith may not fail. And when you have turned back, strengthen your brothers” (vs. 31-32).

“And when you have turned back…” Jesus was telling Simon Peter not only that a test of his faith was coming, but that it was a test Simon would fail.

Simon Peter clearly did not understand, or even believe this prophecy from Jesus. He responded by defending himself, claiming a faith by which he was ready to go to prison, even to death with Jesus.

But Jesus persisted, lovingly but honestly revealing the truth of Simon Peter’s heart, saying “Peter, before the rooster crows today, you will deny three times that you (even) know Me.”

As we read in Luke 22:54-62, this is precisely what happened:

“Then seizing (Jesus), they led Him away and took Him into the house of the high priest. Peter followed at a distance. And when some there had kindled a fire in the middle of the courtyard and had sat down together, Peter sat down with them. A servant girl saw him seated there in the firelight. She looked closely at him and said, ‘This man was with Him.’

But he denied it. ‘Woman, I don’t know Him,’ he said.

A little later someone else saw him and said, ‘You also are one of them.’

‘Man, I am not!’ Peter replied.

About an hour later another asserted, ‘Certainly this fellow was with him, for he is a Galilean.’

Peter replied, ‘Man, I don’t know what you’re talking about!’ Just as he was speaking, the rooster crowed. The Lord turned and looked straight at Peter. Then Peter remembered the word the Lord had spoken to him: ‘Before the rooster crows today, you will disown me three times.’ And he went outside and wept bitterly.”

Why did this have to happen? Why would the Lord allow Peter to go through this test of his faith – a test God knew he would fail?

We remember that in John 16:7, Jesus was very clear with the disciples that the Holy Spirit would not come to them until after Jesus had returned to Heaven. He said to them, “It is for your good that I am going away. Unless I go away, the Counselor will not come to you; but if I go, I will send Him to you.” 

So we know that at the time of this account with Jesus, Simon Peter had not yet received the Holy Spirit in his life, or what John the Baptist described in Matthew 3:11 as a baptism “with the Holy Spirit and fire”. Until that day, Simon’s strength and confidence had only ever been in himself. 

When Simon Peter initially responded defensively to Jesus, he claimed an authority and faith that was based on his own feelings of admiration and loyalty towards Jesus Christ. He was confident in the allegiance he felt towards Jesus, and he sincerely believed that the desire he had to follow the Lord in his own will would be enough.

The fall God allowed in Peter’s life during those hours before the crucifixion was out of His mercy and love for Peter. Simon Peter needed to be humbled. He needed to learn the difference between the empty faith he found in his own strength, and true faith that could only come as he humbled himself, and learned to wait upon the Holy Spirit to come into his life, and to empower and equip him to follow Jesus Christ.

Through this experience of Peter, the reasons for our submission to the Holy Spirit in our prayer lives become evident:

– In our own wisdom and strength, it is impossible for us to save ourselves. As participants in the Christian community, we may work very hard to create an appearance of wholeness and freedom. But without the indwelling of the Holy Spirit in our lives, the sin and deception will continue to maintain its authority over our thoughts and our will.

– In our own wisdom and strength, it is impossible to walk out the steps required to follow Jesus Christ. Without humbly submitting to Him, and waiting for the indwelling of the Holy Spirit, we can not see the fulfillment of the will of God in our lives. On our own, we may manage to do “good” works, but we will miss the mark of the transforming Word of the Father and His kingdom every time.


“Abram believed the Lord, and he credited it to him as righteousness.” Genesis 15:6

“For God so loved the world that he gave his one and only Son, that whoever believes in him shall not perish but have eternal life.” John 3:16

In Ephesians 2:8, Paul writes, “For it is by grace you have been saved, through faith—and this is not from yourselves, it is the gift of God…” In everything we do, we must remember that we are saved – reconciled to God our Father – by God’s grace, through our faith in Him.

Faith means believing the things we read about God in His scriptures. But sincere faith is more than belief alone. Hebrews 11:1 describes faith as confidence in what we hope for, an assurance in that which we do not see.

Faith in God can be compared to the faith we have that the sun will rise each morning. Our assurance in the rising sun is more than a belief we profess, but it is a certainty by which we live out our days. The ways we schedule our hours of work and rest, the timing by which we plant our gardens each Spring, the perspective by which we measure the length of our lives – these things are all based in our confidence that the sun will rise each morning.

This is the faith James was describing in James 2:14-26, when he wrote, “What good is it, my brothers and sisters, if someone claims to have faith but has no deeds? Can such faith save them?… As the body without the spirit is dead, so faith without deeds is dead.”

The kind of faith to which we are called is more than just a particular belief we profess. God’s desire for us is that our confidence in Him be certain, such that our actions, our words, our thoughts, and our perspectives naturally, even unconsciously spring from our assurance that He is all that He says He is.

Remember the promises we find Isaiah 40:27-31:

Why do you complain, Jacob? Why do you say, Israel, ‘My way is hidden from the Lord; my cause is disregarded by my God’? Do you not know? Have you not heard? The Lord is the everlasting God, the Creator of the ends of the earth. He will not grow tired or weary, and His understanding no one can fathom. He gives strength to the weary and increases the power of the weak. Even youths grow tired and weary, and young men stumble and fall; but those who hope in the Lord will renew their strength. They will soar on wings like eagles; they will run and not grow weary, they will walk and not be faint.

In our walk with Jesus Christ, we will face many trials that will force us to consider whether we truly believe these promises. Ultimately, the question we must answer will not be: How many churches did you build? or How many orphans did you feed? According to James, all of our works are simply evidence to the answer to the one, true question:

In everything you did, no matter the trial or darkness you faced, did you put your faith in Me alone?

Sometimes this question will be hard for us to answer. In these times, we take comfort and guidance in the example we find in Mark 9, of the father of the demon-possessed boy. As his son was convulsing uncontrollably on the ground, the man said to Jesus Christ in verse 22, “If you can do anything, take pity on us and help us.”

Jesus answered him, “‘If you can?’ Everything is possible for him who believes.”

The father answered Jesus, “I do believe; help me overcome my unbelief!”

Evidence of Growing Faith:

1 – Private Prayer Life – As we submit to the work of the Holy Spirit in our lives, and experience new freedom and healing, naturally our own faith will deepen. Our own personal transformation through our submission to the work of the Holy Spirit in our lives is the most convincing evidence of the unfailing power of the Holy Spirit to defeat darkness, and to bring new life and freedom.

2 – Intercessory Prayer Life – Another result of the deepening of our faith will be the opening of our eyes to see more clearly the beauty of the image of the Father in other people. But, as our blinders are removed in this way, we will also be able to see more clearly the depth of the suffering and darkness in the lives of people around us.

3 – Exposure of Areas of Weakness – The process of allowing the Holy Spirit to strengthen and deepen our faith will include exposure of areas of weakness – places where we struggle to trust Him. These times may be quite difficult for us, even resulting in a “crisis” of our faith as our doubts and questions are allowed to surface. In these times especially, we must resist the temptation to turn away from God, and instead take our questions to Him, press into His presence in prayer, and meditate on the promises we have in His Word.

Practical Steps towards receiving the indwelling of the Holy Spirit in our lives (Walking out Matthew 16:24)*:

1 – Affirmation of Jesus Christ as the Son of God, and my personal Savior and Lord – Who died for my sins, and Who rose again, defeating death, once and for all. (2 Timothy 1:9-10) (Romans 10:6-9)

2 – Conviction – Prayer for the Holy Spirit to come into my life, and to bring me deeper revelation of my own depravity and bondage to sin, and revelation of the truth of His power and authority to free me from these things. (Romans 3:20 and 7:13-25)

3 – Repentance in the name of Jesus Christ – Prayer for the Lord to create in me a heart of repentance, along with confession of all of the bondage He reveals in my life. (Luke 3:8, Colossians 1:13-14)

4 – Invitation for the Holy Spirit to come into my life, to speak the truth of God’s Word in the places of darkness and broken identity, and to deepen my faith in the revelation of who He is. (John 8:12, Galatians 2:20, Psalm 23:4-5)

*This is not meant to be a one-time “check list” of requirements to receive baptism of the Holy Spirit. These are all steps which will be repeated regularly throughout the life of a believer, as the Holy Spirit leads us into deeper intimacy with and faith in our Lord Jesus Christ.

Week 2 Meditation

Again this week, set aside a total of 1.5-2 hours, 30-40 minutes a day on 3 different days, for prayer. Begin each session this week by going through the Practical Steps listed above towards receiving a deeper indwelling of the Holy Spirit in our lives. Each day read one or two scripture verses listed within the steps for contemplation.

In this week, it may be good to keep a journal as the Holy Spirit begins to bring things up in your spirit. Write down any areas He reveals as places of doubt or deception in your life. Also write down revelations of His Word, which you sense Him speaking into that place. As you are going through the Practical Steps, following are some questions on specific areas that you may consider asking the Holy Spirit to show you.

– What am I trusting to save me that is not You, Father?

– What am I trusting to fulfill Your call in my life, that is not of You? (i.e. money, buildings, houses, my spouse, my children, my education, my reputation, the approval of man)

– In what areas of my life is the Holy Spirit convicting me, and calling me to trust in Him, and to surrender to Him more completely?

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