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Canon Era - Single Fic Arcs
Rheged
Author: McShame
Description: 
Post S5 (AU): canon to the end of S4 & part of the way through S5. 
Gwen and Arthur have been married for several years, Merlin’s magic has been revealed and Arthur has now reached a kind of cold peace with it.  Then a delegation arrives from a kingdom based on magic, and suddenly Destiny is starkly and ruthlessly thrust to the fore.  The question is should - can - it be avoided? 
Word Count: 124,383
Completed: Yes
Comment(s): 
Definitely might want to pay attention to the tags on this one; one scene can be interpreted both as dubious consent (but more like a I want this, but I can’t do this type of situation), as well as mentions of infidelity and attempted suicide by magic because Merlin just doesn’t want to deal with the fallout and aftermath of his and Arthur’s actions and the consequences it has on their relationships with Gwen and Gwaine.  But if you can handle the rough spots, this fic is truly spectacular.  
Whispering Your Name
Author: CaffeinatedFlumadiddle
Description:
A different take on the dorocha.  Instead of them being faceless screams that attack you, they are actually figures of the dead.  Merlin doesn’t quite realize how much death affected him until him and the knights go to close the veil.  
Word Count: 22,517
Completed: Yes
Comment(s):
One of my absolute favorite fics of all time.  It also has a bit of Uther redemption in it and Lancelot lives! It also has one of my favorite interactions in a fanfiction: 
“You’ve got to be kidding me,” Arthur growled, throwing up his hands.  “That thing murdered my people and you allowed it to live--” 
“You murdered my people and I allowed you to live,” Merlin said sharply.  Gwaine felt his eyes widen.  Bold words.  Part of him wanted to ‘ooh’ at it but knew it would lead to a very bad outcome.  
Dower the Stars
Author: RurouniHime
Description:
During a time of great prosperity in Albion, the Druids offer Emrys a precious gift.  Arthur is not amused. 
Word Count: 40,654
Completed: Yes
Comment(s):
A super fun but also very romantic fic.  Druids far and wide come in and kiss Merlin, hoping that their magic will react a certain way with Merlin’s and he’ll bond with one of them.  Merlin however decides to throw a wrench in his plan when he chooses to bond with Arthur instead after almost losing him.  
Overstepping
Author: Masked_Mayhem
Description:
Merlin knew he was pushing his limits, that he was millimetres away from overstepping the invisible line that Arthur had wordlessly set and the warlock had been careful not to cross, but he was never one to listen to the rules that were set for him.  Especially not when he was afraid. 
Agravaine had managed to weasel his way into his king’s mind and ingrain doubts in the people he loved, the people that loved him...doubts that only took place and bloomed as the traitor lied and deceived and planted things against them. He had gotten rid of Gwen easily enough, and had almost gotten rid of Gaius. Merlin was afraid. Were a few words and items all it would take for Arthur to turn against him too?
Word Count: 51,915
Completed: Yes
Comment(s):
Merlin steps over a line and Arthur punishes him for it.  Later, when Merlin was right, Arthur regrets his decision and saves him.  Romance blooms between the two, but a wrench gets thrown in along the way with the reveal of Merlin’s magic and deeds in Arthur’s name.  There is a lot of angst, but I like to feel as if it’s a happy ending for the two.  
Springes to Catch Woodcocks
Author: myashke
Description:
When Arthur pushes Merlin away to protect him, what lengths will Merlin go to remain in his life
Word Count: 83,292
Completed: No
Comment(s): 
Unfortunately the only negative that this fic has going for it is that it doesn’t seem as if it’ll ever be finished.  There are 7 chapters and they were last updated in December of 2011.  Still worth the read.  
Two Souls
Author: Naelyn
Description:
A few days after Camlann, Merlin and Morgana find themselves imprisoned in the same place, and forced to spend their days together.  Basically, this is just a pretext for non-stop Merlin and Morgana interaction once the Emrys reveal has been made. 
“I’ve gone soft over the day, you know.  A few months ago, I would have killed you where you stood.” 
“A few months ago, you did try to kill me where I stood,” Merlin reminded her, and she could hear the smirk in his tone.  
Word Count: 11,417
Completed: Yes
Comment(s):
One of the only fics on this list that won’t be specifically a Merthur fic; but it still isn’t Mergana either.  The idea is that after the revelation at Camlann, one can assume that Arthur lived and that Morgana wasn’t killed; that Merlin had been banished or sent away for the lies he told and somehow was subsequently captured.  
What starts out as a hostile interactions between Merlin and Morgana leads to understanding and apologies that lead on a path to healing.  The end is left open ended, it’s implied that they are sent to their deaths in another kingdom without hope of being rescued, but you can use your imagination to decide if you wanted them to have a happier ending.  
The Patter of Tiny Feet on Cold Stone Floors
Author: TheAvalonian
Description:
When Guinevere finds that she is unable to bear Arthur a child, Merlin offers her the perfect solution: an ancient spell which can create new life out of love, if that love is pure and powerful enough.  But after the ritual, it becomes increasingly obvious that while Gwen has indeed become pregnant, the child she carries might not have been created from the love between Arthur and his wife - but rather from the love between Arthur and his Court Sorcerer.  
Word Count: 79,131
Completed: Yes
Comment(s):
Merlin and Arthur have a baby!  But it’s not an mpreg fic.  Guinevere discovers that Arthur and Merlin are more tied together than she and Arthur are - and while that is difficult for her to come to terms with, she concedes that Arthur has the chance that she never had with Lancelot and doesn’t want to stand in the way.  Queue of course evil plotting on behalf of Morgana and a kidnapping of the queen and princess - who happens to have shown gifts of her own - and it’s a rollercoaster of a tale that leaves you wanting more.  
Metamorphose
Author: clotpolesonly
Description:
When Merlin falls into bed with Arthur, he doesn’t expect to wake up alone.  He doesn’t expect Arthur to give him the cold shoulder either, but there is something else he expects even less which forces him out of the kingdom for over a year. 
He returns to find a traitor in the court, an army on the way, and a love he’d thought all but lost waiting for him with open arms.  
Word Count: 33,753
Completed: Yes
Comment(s):
I don’t usually enjoy mpreg fics because they don’t make sense to me from a biological stand point and usually get explained away as “because reasons”.  This fic is an exception, it does a good job of explaining why it is that Merlin might wound up in his situation and it deals with difficult question about how to handle the knowledge and who to share it with.  
Flowers in the Wind
Author: the_seaworthy_muffin
Description:
A thousand and five-hundred years ago, Arthur Pendragon is sent to the god Emrys as Camelot’s yearly tribute.  He comes to befriend the god, and as the prince continues to spend time on the god’s island, something more seems to blossom between them.  But then the Lady Morgana goes missing, and Arthur betrays Emrys to his father in a moment of misguided trust.  Emrys’ island burns, the heart-broken god refusing to fight for his life.  In dying, he puts a terrible curse upon the prince: to live forever, and never forget. 
A millennium and a half has passed.  Arthur is being slowly torn apart from the inside-out, memories of the past an ever-growing weight in his chest.  When he finally finds Emrys again, he is elated - he’s ready to beg, weep, anything, if only he can find blissful forgetfulness.  But while the god’s power has not faded, his memories have, and he lives his life as young artist Merlin Emrys, believing himself to be a simple man with interesting gifts.  And Arthur’s hopes are dashed.  But there is one last way: Arthur can try, and make Merlin remember again. 
Word Count: 67,366
Completed: No - but it is being continuously updated
Comment(s): 
This is a truly spectacular work of fiction and I almost didn’t give it a chance.  I am so glad that I did.  Honestly, this is now one of my favorite authors on AO3.  
Peace, Plum, Pear
Author: sweetestdrain
Description:
How in his tenth year of rule King Arthur chose a man to take the role of Court’s Magician, and how Arthur made his decision.
Word Count: 13,700
Completed: Yes
Comment(s): 
Merlin fled the kingdom after Uther found out about his magic, and now it’s been ten years since the old king’s death and Arthur’s ascension to the throne, and yet Merlin is still nowhere to be found.  
Arthur gives in and holds trials for the new Court Sorcerer and in walks in an old man named Myrddin Wyllt.  But, there’s more than meets the eye to this strange and mysterious magician.  
Deluge
Author: Suaine
Description:
In the aftermath of Merlin’s battle against Nimueh, the rain seems a minor complication, perhaps even a cleansing influence.  When the rain doesn’t stop, Camelot is pushed to the brink once more.  This time, Arthur may be in over his head.  
Contains: a lot of wet boys in emotional scenes, Arthur knowing more than he lets on, Merlin being an idiot, both of them being a bit stupidly heroic, telepathic chess, rain (lots of), war, making out against a tree, coincidental druids, co-opted history, co-opted myths, magic, coming of age (metaphorically), and more magically annoying yet surprisingly un-floody water than you can shake a stick at.  
Word Count: 50,565
Completed: Yes
Comment(s):
Beautifully written fic, truly a great addition to the fandom. 
Idiosyncratic Romance
Author: F0rcryinoutloud
Description:
“And what about your destiny?” Gaius asked softly.  “Merlin, you know Arthur needs you - whether he realizes it or not.  You won’t have to hide from him forever.”  
Word Count: 13,942
Completed: Yes
Comment(s):
Beauty in the Ashes of our Lives
Author: Fulgance
Description:
After Merlin is executed for Uther’s murder, Arthur’s world falls apart. 
Word Count: 21,599
Completed: Yes
Comment(s):
Arthur makes a huge mistake when he executes Merlin following the reveal of his magic.  
Tiercel 
Author: waldorph
Description:
Arthur is constantly at war. 
Word Count: 6,571
Completed: Yes
Comment(s):
This is a wonderful magic reveal fic where Merlin goes out and discovers more about magic while still taking care of Arthur and protecting him; Arthur is constantly at war because Uther has decided he wants to take over and unite Albion.  
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Reincarnation - Single Fic Arcs
Lovely Ruin 
Author: Naelyn
Description: 
Fifteen hundred years after Camlann, Arthur returns and Merlin is there to welcome him.  Merlin has no idea why he’s back, no idea if it’s pure chance, or destiny, or something even greater - 
All he knows is that the one thing he has spent fifteen hundred years waiting for is finally happening... and he can’t do this.  
“Years ago, you insisted on seeing the good in me before anyone else saw it - insisted on seeing the good in me before even I, myself, saw it.  And now - now Merlin, you won’t even look me in the eye.  So, please, I am begging you.  Tell me, Merlin.  Tell me what’s changed.” 
Word Count: 96,473
Completed: No
Comment(s): 
This fic explores the idea that after fifteen hundred years of an never ending existence of losing people he loves again and again and again, Merlin might not be a whole and healthy, happy individual when Arthur and the knights rise again.  There’s a lot of grief and mourning and death, definitely pay attention to the tags.  It’s a super dark story, but it’s beautiful.  
The Gate of Memory
Author: Destina
Description: 
Merlin forgets to remember, until the time comes to remember once again.  
Word Count: 1,786
Completed: Yes
Comment(s):
This story has Merlin joining a restoration project on the old ruins of a citadel; he has issues with seizures that cause minor hallucinations - that no doctor can explain - and hopes that a retreat to the countryside will do him some good.  There he discovers Arthur, Gwen and Gaius, along with the knights of the round table.  They’ve been reincarnated and aided by a Morgana that has atoned for her past crimes; and he finds out that his seizures and hallucinations are just his memories trying to break back through.  
Scars 
Author: and_damntheconsequences
Description:
After 1500 years, Arthur comes back, and Merlin is finally able to begin healing all the damage those centuries have done.  Secrets fall apart, and for the first time since as long as he can remember, Merlin is both happy and safe.  
But they both know that Arthur must have come back for a reason.  
Word Count: 24,068
Completed: No
Comment(s):
This is a really good fic, but I hope that the author eventually continues on with the story; it was last updated in June of 2020.  
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Modern AU - Single Fic Arcs
Time Forward
Author: kianspo
Description:
While still at uni, Arthur Pendragon meets two people who become his best friends.  he falls in love with one of them... but marries the other.  This isn’t his story to tell; it’s Merlin’s.  And Merlin will always remember that he met Arthur first.  
Word Count: 23,180
Comment(s): 
Definitely a story that will have you laughing and crying along with it, filled with angst and happy endings and just good old fluff and good humor.  
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Canon Era - Arcs
Lantern in the Dark 
Author: Reverie_Indigo
Description: 
After living in Camelot for ten years, Merlin has accomplished nothing - magic is still illegal, Albion remains a mirage, and he’s still just a servant who is lonely and tired of his hopeless pining for Arthur. 
Merlin will pay a heavy price for his lack of direction as Arthur’s walls of denial crumble and Morgana’s plans to destroy Emrys approach fruition.  In his desperation to save the Golden Age of his dreams, Merlin will call upon his magic like never before, testing the old adage that power corrupts - and absolute power corrupts absolutely.  
Word Count: 130,989
Work(s): 3
A Lantern in the Dark 
In the Shadow of the Knight
Plan B
Comment(s): 
This is a phenomenal pair of fics, but unfortunately there was a third in the series called Plan B - or something similar - that I have been unable to find again.  
The Beltane Cycle
Author: astolat
Description: 
There is a story that is not told in Ealdor anymore, not for many years now, a story about Beltane Eve: 
It is said that on Beltane Even when a woman lies with a man - that is not a man - then there will be a fatherless child born from the festivities.  When that child is born their eyes will shine gold with the Old Magic and the Wild Hunt - and its master, Herne - will return the next Beltane and claim them.  
It is said that there was a child born of the Hunt on Beltane Eve in the Kingdom of Camelot twenty one years ago and the mother of that child tricked Herne and the Hunt, keeping the babe with her.  
When Merlin comes of age Kilgharrah warns Prince Arthur Pendragon to fetch his wayward manservant, before the sun sets on his name day, from the forest.  
“A red moon rises over Camelot this night.  The Wild Hunt will ride.” 
Word Count: 27,727
Work(s): 4
Beltane
Coming of Age
That Shall Achieve the Sword
An Exile in Albion
Comment(s): 
This is a very good series, and it just had to make the list.  In this series it explores the concept that Merlin’s powers were not because of his father being Balinor or his destiny, so much as they were because he was fathered by a pagan god on Beltane Eve.  
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Reincarnation - Arcs
The Change Trilogy
Author: emmbrancsxx0
Description: 
Merlin has spent thousands of years preparing for Arthur to rise again.  With the United Kingdom divided after a world war and mysterious killing happening in London, it seems the time has finally come.  
But, Arthur does not rise alone.  
Word Count: 464,257
Work(s): 4
Prologue
Book I: The Spark of Life
Book II: The Twice Crowned Man
Book III: The Same Coin
Comment(s): 
This is truly a phenomenal trilogy - with a prologue that shows all of Merlin’s exploits during the years he spent between Arthur’s death and his rebirth - and it is a definite must read for all Merthur lovers.  
We Begin Again 
Author: katherynefromphilly
Description:
For many long years Merlin waited. 
For the other part of his soul, for the other half of his life.  He was born to serve Arthur.  So that meant he was also born to wait.  Even if it took a thousand years.  Even if the wait seemed to never end. 
Until one day, suddenly, it did.  
When Arthur stumbles from the Lake of Avalon 1,500 years after his death, he finds a world unlike the one he knew.  Faced with the loss of everyone he loved, and the threat of impending prophecy, Arthur must learn what it means to be not just a king, but the Once and Future King.  Merlin does all he can to guide him, even as he struggles to hide his love for his king, and his fear of losing him again.  
Story includes: sass, banter, horseplay & True Love
Word Count: 314,878
Work(s): 4
And like the cycle of the year, we begin again
Our Destinies Our Own
ever onward, through magic, through love
The word you’re looking for is consort
BONUS FIC: The Return of Magic (upon dragon’s wings) 
This fic is essentially a bit of a prequel to the We Begin Again Series, but it can also be read as a standalone.  
Comment(s):
Truly a phenomenal series and well written; one of my absolutely favorites.  Careful because this is definitely a slow burn in the Merthur department.  But, it has endearing Original Characters that are charming and amazing, fitting right in with the story and becoming beloved characters all on their own.  
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Modern AU - Arcs
Loaded March 
Author: Footloose
Description: 
Captain Arthur Pendragon has put together the best team of specialists that the SAS has ever seen, but when his superiors assign Lieutenant Merlin Emrys as his communications officer, Arthur does everything he can to make him feel unwelcome.  Arthur’s job is to protect and guide his team through dangerous missions, and he worries that he can’t do that when the newest member has a mysterious background and acts suspicious when he thinks no one is looking.  
As their assignments become more dangerous, Merlin can’t help but use his magic to keep his team – even is prat of a Captain – safe from threats they couldn’t possibly understand.  But when they are sent on an undercover operation against a group of zealots intent on a magical apocalypse, Merlin needs to confront his fear of discovery and derision, and to finally trust his team with his secret.  
Arthur and Merlin rely on each other for more than the sake of their mission.  The entire world is at stake.  When they learn – from dragons, no less – that they are prophesied to restore the balance of magic to the world, they fight on regardless of the outcome, because duty, honour and loyalty are far stronger driving forces than destiny.
Word Count: 1,261,720
Works: 16
Radioman
War Games
R&R
The Jester
Avalon
Intermission
First Contact
Groundwork
The Play’s the Thing
Means to an End
Desperate Measures
Collaborations
Breakwater
Storm on the Horizon
Do or Die
At the End We Begin Again
Comment(s): 
Don’t let the length of the series dissuade you, it’s like reading the Harry Potter Books, but in the end it is worth every minute spent on it.  This is an amazing series that has me rereading it again and again.  There’s also an entire set of extras that are shorter and part of the same series that Footloose has written to pair along with them.  (Loaded March: Extras)
This series is truly one of a kind with its own cult-like following just like the Merlin series on its own.  
Code Name: Excalibur 
Author: storyforsomeone
Description:
Agent Arthur Pendragon is the best assassin the agency has ever seen, trained and honed to be MI6′s finest weapon.  
He does not need a voice in his ear telling him how to do his job.  He does not need to listen to stubborn geniuses who apparently had no sense of self-preservation and enjoyed baiting professional killers.  He certainly does not fall in love with quartermasters with haunting blue-gold eyes an an irritating habit of saving his life. 
But Merlin has secrets of his own - a heritage he can’t face, and a past he’s been running from for twelve years.  Not to mention the impossible magic coursing through his veins, the likes of which the world hasn’t seen for an age.  
And as London’s days grow darker, as old loyalties are pushed to the breaking point and the fragile trust they’ve built between them is more crucial than ever, Merlin is forced to admit that maybe you can’t run from the past forever, and that secrets always come with a price.  
Word Count: 372,642
Works: 2
Tea and Espionage 
You Only Live Twice 
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