The Cipher of the Forgotten Garden

A fictional origin of the Voynich Manuscript

The Cipher of the Forgotten Garden
by Richard A. Barnett

Chapter One: The Codex in the Ashes

They buried Dr. Adrian Varga under a crooked beech tree on the outskirts of Prague, where the wind always seemed to argue with the bells from the city below. He’d have liked that, nature and noise, colliding in the same breath. I stood back from the grave, clutching the folder he left me like it might burn through my coat.

He was my mentor, my tormentor, and the only person who ever believed the Voynich Manuscript wasn’t an undecipherable joke. “Every code has a pulse,” he used to say. “You just have to find the rhythm that matches your own.”

The mourners thinned after the last handful of soil hit the coffin. Rain began as a polite mist and ended as a confession. I lingered, waiting for silence, and when it came, I crouched down beside the grave. The folder was soaked already, corners softening, the edges curling like old petals. Inside were his notes, his last research drafts, supposedly meant for me. I opened it, and something slipped out: a burnt piece of parchment, no larger than my palm, edges blackened, center filled with symbols too precise to be accidental.

It wasn’t Voynich script. It was his handwriting.

At first glance, it looked like nonsense: scattered letters, dots, and numbers. But I knew his habits. Varga used to hide references inside cross sections of text, using the Fibonacci sequence as a pattern for spacing. I pressed the parchment flat against my leg, the rain slicking the ink into faint smears. The numbers formed coordinates, but not modern ones. They were based on an archaic grid, pre-GPS, something from the 16th century.

“Find the garden,” it read at the bottom, in the smallest, most fragile scrawl I’d ever seen from him. “The truth is buried where the words took root.”

That night I couldn’t sleep. The rain followed me home like a stray. I kept the note on my desk under the glow of an antique lamp, staring at it until dawn cracked the blinds. My apartment was a mess of old texts, half translated pages of the Voynich, and stacks of student essays I’d promised to grade. All of it looked meaningless compared to that burned scrap.

Varga’s death had been ruled an accident. A fire in his home laboratory, faulty wiring, the police said. But there was something odd about the way the manuscript pages he kept in his vault had survived without a single burn.

And now, this.

The next morning, I called the Institute. Varga’s office had been sealed pending the fire report, but his assistant, a nervous man named Pavel, agreed to meet me. “Dr. Keene,” he said, his voice cracking through the receiver, “there’s something you should see before they clear it out.”

I met him in the basement archives, where the air smelled of old paper and ghosts. His hands trembled as he handed me a box labeled simply V. Inside were half charred folders and a single surviving hard drive. But what drew my attention was a sealed envelope taped to the underside of the lid. My name was written on it.

Inside was another note, this one untouched by flame:

“Eliza, The manuscript is not a cipher. It’s a confession. A...”

I froze. My reflection in the metal of the box looked pale and far too young to be standing where he had stood for decades.

A confession.

If the Voynich wasn’t code, wasn’t language, wasn’t nonsense; then what the hell had he found?

The rest of the day passed in fragments: a visit to his burned home, the smell of smoke still alive in the walls, and the eerie realization that his fireplace had been cleaned scrubbed, polished, as if someone wanted to erase something that had been burned there.

As I sifted through the ashes, I found a melted clasp of what had once been a small leather bound journal. Beneath it, hidden by a layer of soot, was a brass key engraved with a stylized leaf.

I knew that symbol.

It appeared on one of the Voynich manuscript’s most peculiar illustrations. A plant that doesn’t exist in any botanical record, growing in a circular pattern, roots intertwined like the arms of sleeping children.

At that moment, I felt the air shift, as if the world had just exhaled.

Someone was watching me.

I turned, but the street outside was empty.

Still, I pocketed the key and whispered to the air, “I’ll find your garden, Adrian.”

When I left, a single page from one of his books fluttered loose from the shelves, landing face up on the floor. The word herbarium was circled twice in red.

And beneath it, written in his hand:

“Bohemia, 1408.”

Chapter Two: The Herbalist
(Alena’s narration begins here, 1408, Bohemia)

My mother said the garden spoke only to those who listened without greed. I was twelve when I first heard its whisper, the sound of sap and sorrow. The Duke’s physician called it witchcraft; I called it memory.

The plants bloomed in shapes that defied reason: leaves shaped like hands, roots that bled when cut. I drew them all, carefully, into a book I kept hidden beneath the floorboards of my workshop.

I never meant for anyone to find it.

Until he came. The stranger from Italy with eyes like tarnished silver and a voice that carried both promise and peril. He called himself Marcellus. He spoke of kings who sought eternal life, of codes that could hide knowledge from the ignorant.

He said my drawings could save lives. He said he could protect me.

He lied.

Chapter Two: The Herbalist (1408, Bohemia)

I kept the door barred that night, though it did little to stop the wind. It slid through the cracks, whispering over my drawings like a jealous ghost. I didn’t trust Marcellus, the Italian. His words were too polished, his hands too clean. But when he laid his map on my table, parchment older than the castle walls, I saw my own handwriting traced faintly over it.

“How did you find this?” I asked.

“I didn’t,” he said, smiling. “It found me.”

He spoke of Prague, of scholars who gathered under King Wenceslaus to study the stars and the elements. He said the Duke’s herbalist, my master, had once been one of them, cast out for trying to preserve the old ways.

“You’re not safe here,” he warned. “Your knowledge is dangerous.”

That part, I already knew.

The women of our village had long been accused of knowing too much; which plant could ease birth, which root could dull pain. The Church called it temptation, the Duke called it heresy. But mothers called it survival.

Marcellus said the king wanted a book. A compendium of every plant that healed and every poison that mimicked it. He said it must be written in code, so no one could misuse it.

“Code?” I repeated. “You mean in Latin?”

He laughed. “No, girl. In something no man of letters could read.”

He showed me symbols and spirals that looked like plant roots and stars at once. “Think of it as music,” he said. “You can hide meaning in rhythm.”

I shouldn’t have trusted him, but he spoke of knowledge like it was a language God forgot to finish.

So I began. I drew each plant as I knew it. The fever herb that cured soldiers, the milkweed that quieted infants; but I twisted the roots, hid the shapes of the leaves, rewrote the truth into mystery. Each drawing became a prayer for the next generation. That they would look upon the page and know, even if no one told them, that healing could come from soil.

But as I worked, something strange began to happen. The plants I drew started to wither in my garden, as if their likeness on the page stole their life from the ground.

Marcellus came often, bringing ink, parchment, and warnings. “They’re searching,” he’d whisper. “Burn your drafts.”

I didn’t burn them. I hid them beneath the old oak in the orchard.

That was the first secret the garden kept for me.

The second came the night the Duke’s men arrived.

They burned my home, shouting that the girl who drew forbidden herbs had betrayed the Church. I ran, clutching the unfinished pages, following the path Marcellus had marked, north, toward Prague.

I reached the gates three days later, half starved, barefoot, but alive. And waiting for me, in a cloaked cart outside the city walls, was Marcellus.

“You survived,” he said, not surprised.

I handed him the pages. “You promised to keep them safe.”

He nodded once. “I will. But only if you finish the rest.”

“What rest?”

He pointed to a blank book in his lap. The vellum bound in green thread, its first page already bearing the faint ghost of my drawings.

The ink smelled of iron.

That was the night I began what would later be called The Voynich Manuscript.

And that was the night I stopped believing knowledge would save me.

Chapter Three: The Garden of Ashes (Present Day, Prague)

It took me three hours to find the garden.

The coordinates from Varga’s burned note led to the edge of the old botanical quarter, behind Charles University, where the cobblestones turned to dirt and ivy claimed the walls like old handwriting. It wasn’t really a garden anymore. More a forgotten patch of green between crumbling greenhouses.

The gate was locked, but rusted enough to give. Inside, the air felt still, heavy with the scent of rain and iron.

I recognized it immediately. Not from memory, but from the drawings. The strange circular beds, the oddly twisted vines. They matched one of the Voynich pages almost perfectly.

I knelt by a cracked fountain where the stonework was etched with the same leaf emblem that had been engraved on Varga’s brass key. I took it from my pocket and turned it in the light. The notches aligned with a small iron lock built into the fountain’s base. One that shouldn’t have been there at all.

The key fit.

When I turned it, something clicked deep inside the stone, and a thin compartment slid open, revealing a small leather case wrapped in linen. Inside were two things: a folded letter, and a sealed vial filled with a dark, amber liquid.

The letter was in Varga’s hand.

Eliza,

If you’ve found this, it means I’ve failed to finish what I began. The manuscript is more than text, it’s a transference. The symbols correspond not to language, but to compounds. The plants drawn within are real, though long extinct. But they were bred to remember; coded through pigment and proportion. Whoever understands them can recreate them.

And someone already has.

You must find the original pigments. The formula was hidden in a letter dated 1408, written by the herbalist herself. I’ve traced one surviving fragment to the archives beneath the Clementinum.

Be cautious. They know you’re looking.

— A.

I looked at the vial. The liquid glowed faintly when it caught the light. It wasn’t paint. It wasn’t blood. It looked almost alive.

The Clementinum was only a few blocks from where I stood. A vast Baroque complex that once held the Jesuit library and now housed rare manuscripts. I’d been there before, years ago, when I was still Varga’s student. The thought of returning sent a cold knot twisting in my stomach.

Still, I had to go.

By the time I reached the archive entrance, the afternoon light had gone thin and gray. I flashed my credentials at the guard, who barely looked up. The basement smelled like history and dust. A scent that always made me feel both reverent and claustrophobic.

I found the section marked Bohemia: Early Herbal Studies, 1400–1500. The drawers were heavy, the kind built for maps and manuscripts too delicate to bind. I pulled one open and froze.

There it was.

A single sheet of parchment, sealed in glass. The script was familiar; looping, feminine, precise. The bottom bore a name I recognized from the few legible words in the Voynich manuscript itself: Alena Vlasáková.

The fragment read, in rough translation:

“We write to preserve what men destroy. When the flames come, may the garden remember us.”

As I stared at the text, a soft sound echoed behind me. A footstep.

I turned.

A man in a museum uniform stood near the entrance, but his face was unreadable. “Closing soon,” he said.

I nodded, slipped my phone into my bag, and pretended to leave. But as I reached the door, I caught sight of him in the reflection of the glass case. He wasn’t watching the clock. He was watching me.

When I left the building, the sun was gone and the streetlights flickered on one by one. The air smelled faintly of smoke again.

My apartment felt foreign when I returned, as if someone had been inside while I was gone. Papers had shifted. A coffee mug had moved. And on my desk, where I’d left the brass key, lay a single pressed leaf — pale, veined, almost translucent.

It was the same shape as the one on the Voynich’s final page.

I stared at it for a long time before whispering the word that had been circling in my head all evening:

“Alena.”

The garden wasn’t just a metaphor.

It was real.

And somehow, she was still speaking.

Chapter Four: The Pigment Formula (Present Day)

I didn’t sleep that night. Every time I closed my eyes, I saw that pressed leaf, pale and delicate, lying on my desk like a message from the past. I didn’t know who had left it, or how they’d entered my apartment. The locks hadn’t been forced.

By dawn, I’d packed a small satchel: the vial, the brass key, and Varga’s letter. I needed answers, There was only one person who might help me interpret the chemical side of what he’d found — Dr. Lukas Reiner, a forensic chemist I’d once dated during my graduate years, before ambition replaced affection.

He didn’t look surprised to see me when I showed up at his lab. “You only call when something’s burning,” he said.

“Something is,” I replied, handing him the vial. “Tell me what this is.”

He held it up to the light. “Looks like plant resin mixed with a metallic compound. Almost phosphorescent.”

“Can you analyze it?”

He smirked. “When have I ever said no to you?”

While he ran the sample, I sat at his desk and opened my laptop. The Voynich Manuscript’s pages glowed on the screen scanned and magnified, digital ghosts of ink and parchment. I compared one particular folio to the pressed leaf from my desk. The veins matched perfectly, down to their spiral pattern.

That’s when I saw it.

In the background of the drawing. behind the vines and roots, faint geometric shapes repeated in rhythm. I adjusted the contrast until they stood out like hidden music notes. A series of twelve recurring patterns, each resembling a constellation.

Varga’s words echoed: It’s not a cipher. It’s a confession.

Lukas returned, holding a printout. “You’re not going to like this,” he said. “The compound’s base is an extinct plant resin. The metallic trace; mercury, gold, and chlorophyll. That’s impossible, but it’s there. Whatever this is, it’s alive.”

“Alive?”

He nodded. “Some kind of bio luminescent reaction. It responds to ultraviolet light.”

He flicked off the lab lights and turned on the UV lamp. The vial began to glow faintly green, and when I rolled it between my fingers, a pattern shimmered on my skin; faint script, curling and fading like whispers.

“Lukas,” I whispered, “record this.”

The letters formed just long enough for me to read two words: Clementinum vault.

The same archive where I’d found Alena’s fragment.

That’s when the door behind us clicked open.

A man stepped inside. The same uniformed figure from the library, only now his face was uncovered. Pale eyes. Thin smile.

“Dr. Keene,” he said softly, “you were told to leave this alone.”

Lukas reached for his phone, but the man raised something small. A vial identical to mine and dropped it. The smell of bitter almonds filled the air. Gas.

We ran.

By the time we burst out into the courtyard, my lungs were on fire. Lukas grabbed my hand, coughing. “Who the hell is that?”

“I think,” I said, catching my breath, “they’re the ones who’ve been keeping the garden buried.”

Chapter Five: The Binding Ink (1408, Bohemia)

Marcellus said we would hide the pages inside a monastery. “The safest place is where no one questions faith,” he said.

I no longer trusted his faith.

We’d been working for months in secret, under candlelight, mixing pigments made from herbs that should never touch one another. Each plant had meaning. Not just medicinal, but emotional. Pain leaves traces in the ink, he said. So does fear.

When I asked him who he worked for, he only smiled. “For the ones who understand that truth must be protected from the unworthy.”

But one night, as he slept, I found a letter in his satchel bearing a seal. Two interlocking circles and a stylized leaf. The same emblem engraved on his ring. The same one, centuries later, would end up on Varga’s key.

The letter was addressed to The Order of the Green Flame.

Its contents were brief:

The girl’s work progresses. She doesn’t yet understand the full purpose. The formula will outlast us all.

I read it twice, then burned it.

He woke before dawn, and I told him nothing.

We finished the final section that week. The “botanical diagrams,” he called them. He made me ink them using a special mixture of crushed leaves and powdered stone. “The color will never fade,” he said. “Because the ink itself remembers.”

But it wasn’t until I pricked my finger and a drop of blood fell into the mixture that the ink changed color — from green to a shimmering gold.

Marcellus stared at me in awe. “You’ve done it,” he whispered.

I didn’t understand what I’d done until later, when he vanished with half the manuscript and the Duke’s guards arrived the next day.

They asked me where the “forbidden book” was. I told them I’d burned it. They didn’t believe me.

I was imprisoned for treason, accused of sorcery, and left to rot in a cell that smelled of moss and old prayers.

But I hadn’t lied. I’d burned half the pages. The half I’d rewritten after learning Marcellus’s secret.

What remained, hidden in a root cellar beneath the convent, was the true version, the one written in my own hand.

And in its final margin, I left a warning:

To whoever finds these pages, remember that knowledge grows only where truth is planted. The garden watches.

Chapter Six: The Order of the Green Flame (Present Day)

Lukas and I holed up in a small flat near Vinohrady after the gas attack. The police didn’t believe our story. “A man in a uniform” wasn’t enough to open an investigation. I was beginning to think it wouldn’t matter. Whoever he worked for, they were already ahead of us.

We went over the evidence again: the vial, the glowing script, the coordinates. I opened the scanned Voynich folios again, and this time, Lukas noticed something I’d missed.

“See that pattern between the vines?” he said. “That’s not random. It’s a Fibonacci spiral.”

He traced the line with his finger. “Each turn corresponds to a symbol — if you plot them numerically, you could get a sequence.”

We did. The numbers formed a set of letters: A V L A.

I stared at them. “Alena Vlasáková.”

We cross referenced her name in the Prague archives. She’d been tried for witchcraft in 1412. Executed. But her grave was never found.

When we returned to the old garden that night, someone had already been there. The soil was freshly turned, as if someone had dug and left in haste. Lukas unearthed a fragment of pottery and a rusted clasp, identical to the one I’d found in Varga’s ashes.

Inside the clasp was a sliver of parchment, nearly disintegrated. Written in faint brown ink were words that made my pulse stop:

The garden is not a place. It is a code.

Chapter Seven: Confluence (Both Timelines)

(Alena)
The guards came for me on a moonless night. I thought they meant to drag me to the gallows, but instead they took me to the royal apothecary. The King himself sat among scrolls, pale and trembling.

He held the half of the manuscript Marcellus had stolen. “Tell me,” he said, “does this grant immortality?”

I almost laughed. “No, my lord. It grants understanding.”

He looked disappointed. “Then burn it.”

They threw it into the fire while I watched. The ink did not burn. It shimmered, then turned to ashless smoke — like breath leaving the body.

When I was returned to my cell, I knew they would kill me soon. So I used what little blood remained in my veins to finish my confession on the wall: the cipher to my garden. The code was simple: twelve plants, twelve constellations, twelve letters of truth. Whoever read the rhythm could find me.

(Eliza)
Lukas and I discovered the same pattern. Twelve repeating symbols hidden in the manuscript’s margins. The sequence matched twelve celestial coordinates, each pointing to historic monasteries across Europe.

But one stood out: a location in southern Bohemia.

“Where she died,” I whispered.

We drove through the night, following the GPS to an overgrown ruin outside Český Krumlov, a crumbling convent. In the courtyard, the earth had been disturbed.

We dug until dawn.

Our shovels struck stone. Beneath it, a box bound in iron, its lid engraved with the leaf emblem. Inside, wrapped in linen and preserved by resin, lay a single folio, the final missing page of the Voynich Manuscript.

And in the center of the page, written in faint gold ink, were twelve words.

The garden endures. Truth grows in those who listen.

Chapter Eight: The Voice in the Ink (Present Day)

We sealed the folio inside a protective case and drove back to Prague before the sun rose. The city was still half asleep, fog curling over the Vltava like memory itself. I didn’t speak; Lukas didn’t either. The weight of that page felt alive between us.

When we reached my apartment, I placed it under the UV lamp. The faint gold ink brightened immediately, shimmering like it was breathing. I photographed each segment, then began cross referencing them with the manuscript scans.

The pattern wasn’t random. It was recursive. Each symbol mirrored another elsewhere in the book, forming loops that repeated in mathematical precision. It was like the manuscript was responding.

“Look at this,” Lukas said, pointing to one of the spirals. “If we overlay these twelve coordinates on the Voynich star charts, they align with the zodiac—but inverted.

He wasn’t wrong. When we mapped them in reverse, the letters spelled one word: Vlasáková.

At that moment, the room flickered. The UV lamp dimmed. The vial of pigment on my desk began to glow faintly again, pulsing in rhythm with my heartbeat.

And then, just for a second, I heard a sound.

It wasn’t quite a voice. More like the echo of ink being written. The soft scrape of a quill.

Lukas looked at me. “You heard that too, didn’t you?”

Before I could answer, a knock came at the door.

The same man from the archives stood there, calm, unbothered, the faintest smile on his lips. “Dr. Keene,” he said, “the Order thanks you for finishing what Dr. Varga began.”

I stepped back. “Who are you?”

He didn’t answer. Instead, he looked past me at the glowing folio. “You’ve opened the last seal. That knowledge cannot remain free.”

Lukas moved between us. “If you touch her...”

The man sighed. “You don’t understand. This manuscript was meant to protect. Every age has tried to unlock it. Every time they did, people died. The Green Flame exists to keep it contained.”

“Contained?” I snapped. “It’s a book, not a weapon.”

He looked almost sad. “That’s what Alena thought too.”

He turned and left without another word.

Chapter Nine: Alena’s Confession (1408, Bohemia)

They came for me the night after the manuscript was burned. I expected death. Instead, I was taken to a cloister deep within the forest, where a single candle burned before a symbol carved in stone. The leaf, the twin circles.

Marcellus was there.

“You lied,” I said. “You gave them my work.”

He bowed his head. “And I lost it. But I saved you. The King believes you’re dead. You’ll stay here, hidden. Finish the true book.”

“I won’t.”

He placed a small wooden box before me. Inside was a vial of golden ink. The same mixture I’d once bled into. “Then you’ll die with it. The ink binds to you. It remembers your pulse.”

He left, locking me in.

For days I sat in darkness, listening to the wind move through the cracks. I thought of my garden, of the way the earth hummed when rain touched its roots. And I understood.

The manuscript had never been about immortality. It was about memory. The pigments, my pigments, contained encoded botanical DNA. When mixed, they could revive extinct flora, recreate the plants as they once were. A perfect resurrection.

But in the wrong hands, that same formula could weaponize nature itself. Plagues, poisons, power.

So I finished my confession not as an instruction, but as a warning. I used my own blood to mark the final page. The one that said:

"The garden endures. Truth grows in those who listen."

I sealed it inside a box, buried it beneath the cloister, and carved the coordinates into the wall. Then I drank what remained of the ink.

It was bitter and bright and full of memory.

They called it death. I called it preservation.

Chapter Ten: The Garden Remembers (Present Day)

Lukas and I traced the Order’s crest through old archives. It appeared in royal ledgers, Jesuit records, and pharmaceutical patents. The Green Flame had evolved into a modern research foundation. One that quietly funded bioengineering under the guise of conservation.

And Varga had worked for them.

He must have realized too late what they wanted: to replicate Alena’s formula, to bring extinct species back. And possibly something worse.

We followed the trail to a disused greenhouse on the outskirts of Prague, once owned by the Order’s front company. Inside, the air was warm, heavy, and humid. The walls were lined with glass tanks filled with soil and glowing roots.

They had already begun recreating her garden.

Each plant matched a drawing from the Voynich folios, yet each shimmered faintly under the UV light as if remembering its source.

At the center stood a vat marked Prototype 12. Inside floated something like a flower, suspended in viscous amber. Its petals formed the exact shape of Alena’s symbol.

“Lukas,” I whispered, “she’s here.”

Before we could move closer, a voice echoed behind us, the same man from the archives. “You should never have come.”

I turned, holding the vial. “You wanted this? Take it.” I threw it into the nearest tank. The liquid spread through the soil like wildfire.

The glow shifted. The plants began to move, curling and collapsing as if exhaling after centuries of being held still. The air thickened with pollen and light.

Lukas grabbed my arm. “Eliza, we have to go!”

We ran as the greenhouse erupted behind us. No flames, no explosion, just a soft, blinding luminescence that swallowed everything in silence.

When I woke, dawn was breaking. The greenhouse was gone. Nothing but soil remained, dark and clean, as if the earth had reclaimed its secret.

Lukas sat beside me, dazed but alive. “What did we do?” he whispered.

“We let it remember,” I said.

We turned to see, in the distance, a single sprout pushing through the dirt — small, green, and impossibly alive.

Later, when the authorities arrived, they found nothing dangerous, nothing traceable. Only a patch of new growth where no seed should’ve taken root.

I went back to my apartment, opened my laptop, and looked again at the Voynich scans. The pages had changed slightly — new markings along the edges, faint but unmistakable. Words, this time, written in English.

THANK YOU.

I stared for a long moment, then closed the file.

The manuscript was no longer a mystery to solve. It was a memory set free.

I walked to the window. The sun broke through the clouds over Prague, painting the rooftops gold. And in the courtyard below, beneath the crooked beech where we buried Varga, the grass shimmered faintly in the morning light — as if remembering.

Epilogue

Months later, I received a package with no return address. Inside was a blank notebook bound in green thread. When I opened it, the first page bore a single hand written line:

Every code has a pulse. You just have to find the rhythm that matches your own.

I smiled, placed it on my shelf beside the others, and whispered into the quiet room:

“The garden endures.”

The End