Clearing the Fog: How the Holy Spirit Restores the Mind
I was jogging when a troubling thought popped into my head in a flash. I had been doing everything right: exercising, eating healthy, and avoiding chemicals. On the outside, I seemed to be doing well. But inside, something didn’t feel right. I stopped running because I couldn’t continue.
Why does our mind feel so heavy and confused even when we're trying our best to be healthy?
Since my early teens, I’ve wrestled with what felt like low-grade depression. I pretended everything was fine by smiling, talking and keeping things cheerful. But when I was by myself the real struggle started. My thoughts turned dark. Memories I didn’t want would flash in—failures, regrets, awkward moments. They would replay like a broken record, and I couldn’t hit pause. Sometimes the fog would lift in a few hours. Other times, it lingered for days, and with it came a frustrating mental sluggishness.
I used to be a dedicated student. At first my grades were great but as the schoolwork got harder my results didn’t reflect the effort I was putting in. This made me feel even more confused. Even the activities I used to enjoy like art and sports began to feel dull and unexciting.
Over time, through studying RAPT Nakamura’s teachings, I began to see that this wasn’t just about mental health or brain chemistry. It was spiritual. Scripture tells us that Satan is the ruler of this world (John 12:31), and he works through deception, distorting truth and attacking the mind. He uses subtle, daily tactics to wear us down—through media, culture, even the institutions we’re supposed to trust.
The things that should bring life—art, education, family—often end up draining us. Entertainment leaves us feeling empty. Schools, instead of nurturing hope, sometimes foster pressure and despair. Homes, which should be havens of love, too often become places of criticism and wounds. Even religion, when disconnected from truth, can mislead people. In Japan, where I live, shrines and temples outnumber convenience stores. Religion is everywhere, yet few recognize that casual participation in idolatry—even something as simple as clapping hands at a shrine—can have spiritual consequences.
Of course, brain fog isn’t only spiritual. There are physical and environmental factors too. A diet high in additives and sugar pollutes the body and the mind. City life limits fresh air and natural rhythm. These things matter. RAPT-san teaches that physical stewardship, especially caring for the brain, is essential to spiritual growth. (I explored this in more detail in a recent Medium post: "Clearing the Fog".)
But here’s the difference: the world offers quick hacks and habits. God offers transformation.
When I first came across RAPT-sans blog, one article stood out to me: “The Best Way to Combat Depression Is to Make Your Brain Work Faster”. The idea surprised me—but it made sense. Like athletes train their bodies, we can train our minds. And not just with mental exercises, but by learning how to activate the brain through spiritual growth.
Through the revelations RAPT-san had received from God, I began to understand that we were created in God's image, and that includes the capacity for divine-level intelligence (Genesis 1:27). But because we've been disconnected from God, we simply didn't know how to unlock it (related post).
The turning point came when I learned that the Holy Spirit has the power to activate our brains, giving us greater clarity, faster thinking, and stronger discernment. As RAPT-san explains, we can receive the Holy Spirit in abundance through prayer, Bible study, and consistently applying God’s Word (source; source).
This is not just about "feeling better." It’s about being renewed in both mind and body. As your soul grows and is filled with God’s Spirit, fatigue lifts, thoughts sharpen, and even the mental dullness we often blame on aging can disappear (source).
In today’s world, our attention is scattered—students are buried in schoolwork, adults in endless tasks. This constant noise drowns out our spiritual sensitivity. But even small changes—like choosing to spend your free time seeking God—can bring a dramatic shift in your mental and emotional state (source; source).
Prayer calms the nervous system. Worship displaces fear and anxiety. And the Word of God rewires the brain, replacing lies with truth (related article). Over time, you’ll find yourself thinking more clearly, worrying less, and moving through life with renewed focus and peace.
We are not powerless. RAPT-san declares that everyone can improve their brain function—not just recover from brain fog—through the Word and prayer. And if you think, “I can’t do it,” that voice is not from God. That’s deception from the enemy (source).
It’s true—mental fog and depression can feel overwhelming. But I came to realize something crucial. As long as I saw myself only as a victim of my circumstances, I remained stuck. One of the most eye-opening teachings from RAPT-san was this: “Most of the problems in this world are the result of human sin.”
That truth pierced me. Instead of asking, “Why is this happening to me?” I started to pray, “Lord, show me what’s within me—what sins, fears, or hidden attitudes are keeping me in bondage.” And every time I’ve prayed that way, God has responded with healing and joy (source).
Contrast that with the world’s message: “Follow your feelings.” “Do what makes you happy.” “You are your own truth.” These affirmations might sound positive, but they offer no real foundation. They don’t lead to transformation—only deeper confusion.
Meanwhile, RAPT-san has endured relentless persecution for standing firm in the truth. In today’s climate, it would be easy—even expected—for someone in his position to break down mentally. And yet, after decades of spiritual training, he remains grounded, joyful, and full of wisdom. Why? Because he has trained his mind to think like God—to solve problems without being ruled by emotion (related testimony).
Through his life and teachings, I’ve come to understand that true strength doesn't come from motivational quotes or self-help books—it comes from spiritual growth. When we think like God, we live with peace, hope, and clarity, no matter the challenges we face.
And this is the heart of Jesus’ words in Mark 12:30: “Love the Lord your God with all your heart and with all your soul and with all your mind and with all your strength.” Every moment of our lives is a gift to be used drawing closer to God, training our minds and spirits to walk in truth.
It’s not an easy path. But in this journey, there is joy. In the repentance, there is freedom. And in the daily discipline, there is unshakable confidence that God is truly with us (related testimony).
This journey didn’t change me overnight. But over time—through daily spiritual practices like prayer, Bible study, praise, and sharing the gospel—my mind began to clear. The fog that once felt constant started to lift. And now, mental clarity has become my new normal.
Of course, there are still moments when the clouds roll back in. But when they do, I know what to do: I return to the Word, I call upon God, and I begin to recover. It’s like a reset for my spirit—and it works every time.
This clarity has helped me avoid unnecessary mistakes and negative thought spirals. Even something as simple as jogging, which once left me feeling heavy and emotionally drained, now brings joy and renewal. Occasionally, I’m so moved by the presence of the Holy Spirit that I stop in my tracks—not from despair, but from awe.
Yes, aerobic exercise is good for the brain. But when it's connected to the ultimate purpose of life—drawing nearer to God—it becomes something far more powerful.
If your mind feels cloudy, don’t settle for coping. You were made for clarity. The Holy Spirit is the Spirit of truth, and can bring light into every shadowed place of the mind.
You don’t have to walk through this fog alone. The same Spirit who transformed my life is available to you. All it takes is a willingness to seek, to ask, and to surrender.
If this message spoke to you, I encourage you to explore the teachings that helped open my eyes. The RAPT- blog is filled with truth and practical wisdom for those hungry for deeper understanding and lasting transformation.
Image by: Emma Simpson on Unsplash
