God Prepares the Soil: How God Uses Pain, Darkness, and Truth to Heal Our Hearts
- Hannah
- 4 days ago
- 7 min read
Why Does God Allow Darkness and Pain? Root-Level Healing: How Jesus Transforms the Deepest Wounds and Restores the True You
The soil of the soul is never shaped in ease. It is tilled in darkness, watered by tears, and broken open before anything new can grow. Today, as I listened to Psalm 6, I heard David’s voice trembling through the centuries, “I am weary with my moaning; every night I flood my bed with tears… my bones are troubled” (Psalm 6:6–7). David knows he has sinned. He knows his enemies are circling. Yet he still cries out boldly, “Depart from me, all you workers of evil, for the Lord has heard my weeping.” God accepts his prayer. God hears his plea. And the ones who hunted him become the ones who tremble.
David isn’t unshaken because he is strong — he is unshaken because he goes to God.
As I reflected on this, a childhood memory surfaced. My sister loved The Lion King. She used to prowl and roar on the back of the sofa, fully convinced she was a lioness. The musical score from the elephant graveyard scene, when Simba is surrounded by bones, darkness, and hyenas, mirrors Psalm 6. Simba is chased by death, just as David was chased by enemies, just as we are chased by spiritual darkness. But then Mufasa appears. A mighty lion. A rescuer. A father who steps into the graveyard and breaks the power of fear. God does the same for us. When I look at so many healing journey's and my own, I see the same pattern, the truth, Scripture reveals. The darkest seasons are not then end of life, they are the very soil where God prepares transformation.
The Ground We’ll Cover
In this post, we’ll explore:
Why God uses darkness to prepare the soul
How pain creates the desperation that leads to healing
Why hidden lies must surface before real change can begin
How Jesus addresses the root cause—not the symptom—in every encounter
What root-level healing looks like in our modern struggles
My experience going through this process
Darkness Makes Light Impossible to Ignore
The dark is the contrast to the light. The darker it is the more the smallest pinprick of light is visible. In the places that feel hopeless, scary, and isolating the darkness focuses you. You can't see anything besides the light because the darkness has taken away everything else, all the distractions or ways that you had gotten by before. The darkness forces you to look for the one thing that can lead you out.
Jesus said, “I am the light of the world. Whoever follows me will not walk in darkness, but will have the light of life.” (John 8:12)
In the dark, there is only one beam of light — Jesus. You follow Him because nothing else can be seen. Nothing else can save. Nothing else can guide.
This is why the valley matters. “Even though I walk through the valley of the shadow of death, I will fear no evil, for You are with me.” (Psalm 23:4)
Darkness becomes the place where the presence of God is unmistakable.
Pain Creates Holy Desperation
Pain makes us move. Pain makes us seek. Pain makes us desperate for healing. People in pain, physical, mental and spiritual, seek out new things they haven't tried. They hope in things that provide promise of relief and of healing.
Throughout Scripture, people in pain did whatever it took to reach Jesus:
The woman who pushed through a crowd just to touch His robe (Mark 5:27–29).
The blind men who cried out louder when others told them to be quiet (Matthew 20:30–34).
The paralytic’s friends who tore open a roof to lower him before Jesus (Mark 2:4–5).
Pain removes pride. Pain removes pretense. Pain makes us willing to try what we’ve never tried before, because the old ways no longer work.
And when human solutions fail, we finally seek the miraculous. The impossible. Which is God’s specialty.
Jesus said, "With man it is impossible, but not with God. Fo all things are possible with God." (Mark 10:27)
The Ugly and the Pain Must Surface Before It Can Heal
The darkness, the pain, the lies all come out in order to be healed. They are like shrapnel, left buried in the body, it festers, moves, infects and harms. An infection isn't who you are, it is a symptom of something that is present that isn't who you are. It's something foreign that doesn't belong there.
When we start the healing treatment of seeking truth, it's not a pretty or gentle experience. It's like doctors having to cut into a wound that healed but is festering underneath and cleaning it and cleansing it. This process often reveals shame, sin, lies, and false identities we carried that were put there by someone else, an enemy of our souls.
These are the root causes of the pain and suffering that has been our lives for so long. We accepted lies and based our existence and behavior on false beliefs that we were unlovable, not enough, can't be forgiven, can't be good enough for God, or that God hates us. These lies only benefit one thing - Satan. They don't benefit you, they keep you bound up, sick and captive.
But when truth surfaces, lies lose their power. The enemy’s voice is unmasked. And the foundation we’ve been living from is finally revealed. That is why Jesus never treated just the symptoms. He always went straight to the heart:
To the lame man — “Do you want to be healed?” (John 5:6)
Jesus wasn’t asking about physical mobility. He was asking about the man’s entire life. For 38 years, this man’s identity had been shaped by immobility. His routines, relationships, expectations, and even his sense of self were built around being unable to walk. Healing would not just change his legs, it would change everything.
Jesus went to the root: Do you actually want the responsibility, the freedom, the change, the identity shift that healing requires? This wasn’t about legs. This was about the heart.
To the woman at the well — “You have said the truth.” (John 4:17–18)
Jesus didn’t shame her. He didn’t lecture her. He didn’t list her sins. He simply named the truth she had been hiding under layers of rejection, abandonment, and relational pain. Her real wound wasn’t her relationship history — it was her thirst to be seen, known, and valued.
Jesus went to the root: You’re not unlovable. You’re not invisible. You’re not beyond redemption. I see you. I know you. And I’m offering you living water, the thing you’ve been searching for your whole life. This wasn’t about her past. This was about her identity.
To the woman caught in adultery — “Neither do I condemn you.” (John 8:11)
Her deepest wound wasn’t the act of adultery, it was the crushing weight of shame, public humiliation, and the belief that she deserved death. Jesus didn’t just save her life. He saved her dignity.
He went to the root: Your accusers are gone. The shame is broken. You are not defined by your worst moment. Now walk free, not just from sin, but from the identity that sin tried to give you. This wasn’t about the scandal. This was about her restoration.
To the rich young ruler — “Sell what you have.” (Matthew 19:21)
Jesus wasn’t attacking wealth. He was addressing attachment. This man’s wound wasn’t greed, it was that his identity, security, and sense of righteousness were rooted in possessions and performance.
Jesus went to the root: Your wealth is not the problem. Your dependence on it is. Let go of what owns you so you can receive what frees you. This wasn’t about money. This was about surrender.
Jesus exposes root of all your heartache that we can't see, of what we may not even know ourselves. He never treats symptoms because symptoms aren’t the problem, they’re the evidence of the problem. He goes to the root so He can heal the root.
This Process is Messy
Just like gardening or surgery, this process is messy. It's not gentle or easy. It's full of pulling weeds, scraping out infection, getting your hands dirty and feeling exhausted at the end of it. It's ugly - all you see is the dirt and the dying weeds or the used bandages. It's hard to see the garden or healed scar that is in the future.
God tells us, "For I know the plan I have for you, declares the Lord, plans for welfare and not for evil, to give you a future and a hope (Jeremiah 29:11)".
We can't see the future no matter how much we think we can. Nothing in our lives has ever turned out the exact way we thought it would (and thank God for that!). Like a master Gardner or surgeon God has a plan for a thriving garden and a healed wound, it just takes the work to get there.
Healing is the best work you will ever do an you will never do it alone. God, the great healer and God of the impossible - the way, the light, and the truth - leads you every step of the way.
Closing Thoughts: I Experienced This
For years I cycled through the same patterns that caused me pain: codependency, perfectionism, people-pleasing, self-abandonment, selecting narcissistic partners and people to trust, and basing my identity on how well I performed.
Every heartbreak, every critical inner thought, every idea that I would be better off not here piled on that it was me, who I was, that was causing this. That these things were who I was, and not who God had told me I was. I struggled with this until I was 40 years old.
But God (these words are in the Bible when we are notified God is working - he's always working, we just fail to notice many times), changed it all for me. I got to my darkest, my weakest, my most dire time in life and was guided by the smallest truths that led to bigger and bigger ones, unraveling, breaking, and shedding the lies that had been piled on me and were not mine to carry or live by.
"Behold, I am doing a new thing; now it springs forth, do you not perceive it? I will make a way in the wilderness and rivers in the desert." (Isaiah 43:19)
This awareness set me free from the burdens that so many of us carry unknowingly until the darkness shows us the light, pain calls us to seek true healing, and the root cause is addressed. I pray that whoever is reading this can see that darkness is not the end, it's the tilling of the soul/soil in order to remove the weeds and sow truth, freedom, love, and joy.
💛 Hannah
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