Disclaimer: I do not own Fairy Tail, or any of its associated characters and lore. That right belongs to Hiro Mashima.
Magnolia Town, Kingdom of Fiore, Ishgar, Earth Land, April, X686
When Mavis Vermillion was six years old, she had to come to terms at a young age that she was stranded and alone on Tenrou Island after the Red Lizard Wizard Guild she had an uneasy relationship with was wiped out and robbed by the Dark Guild known as Blue Skull. Growing up with an abundance of Magical knowledge from the books that remained, Mavis, nonetheless, grew up to be an intelligent and determined thirteen year old that sought to see the greater world and get even with Blue Skull if, for nothing else, than in memory of her would've been friend Zera who died as a result of the previous Guild War.
That was when the three Sylph Labyrinth Treasure Hunters, Yuri Dreyar, Precht Gaebolg, and Warrod Sequen came to Tenrou Island in search of the stolen Tenrou Jade which Mavis bargained with the trio in exchange for their aid in taking down Blue Skull at least and leaving the island at most. Upon initially arriving at Magnolia Town, however, the team of four were soon enough driven out by Blue Skull which prompted Mavis, Yuri, Precht, and Warrod to seek help from a more experienced Wizard that Mavis quickly learned from her own analysis as well as the Wizard's own confession that he was the infamous and immortal Zeref himself.
With Zeref's aid, Mavis became stronger in Magic while her unlikely friends awakened their own Magic Power and together, as one team, successfully struck back against Blue Skull. However, upon learning of the dangerous effect the Tenrou Jade had on people, Mavis was quick to use the spell, Fairy Law, that she herself had created from a lifetime of Magical study from both books and Zeref's teachings alike to destroy the jewel once and for all, but had promised a skeptical Yuri beforehand that the efforts of him and his partners wouldn't go to waste.
With the conflict with Blue Skull over and done with, and the four developing Wizards having recovered from their struggles, Mavis then gathered the money the vanquished Dark Guild had hoarded and made an offer to her friends that would allow them to move forward and get Magnolia back on it's feet: form a Dark Guild of their own.
"How does that make any sense at all?" Yuri could not help but say on behalf of his treasure hunting comrades who were just as gobsmacked as he was.
Mavis merely shrugged with a seemingly innocent smile as she responded. "I don't want to repeat Blue Skull's misdeeds, but I do not want to follow the Magic Council's rules either. It will not be easy at first, but it's my hope that what we'll start here will create both a comfortable economy for Magnolia and a home that anyone could return to."
Sharing a glance amongst themselves, the three older men soon smiled at each other as they turned back to Mavis.
"Have you thought of a name, Master Mavis?" Warrod asked with a slight joking emphasis on the way he referred Mavis.
Mavis' own smile broadened as she answered. "Fairy Tail. For no matter how dark our paths will take us, this will be the start of an endless adventure."
Fairy Tail Guildhall, March, X696
Almost ten years had come and gone since Fairy Tail was founded, and the Dark Guild had risen to prominence in Fiore through its own successes in the Second Trade War that erupted in July of the same year it was founded. Under Mavis' leadership, the governmental powers of Ishgar from Fiore's own royal family to the Magic Council itself had given the christened Fairy Tactician and her guildmates a wide berth as they acquired territory and subjugated one guild after another.
A month before the guild's tenth year anniversary, though, its members were celebrating the recent birth of Makarov Dreyar, Yuri's own son through his wife of six years, Rita, that Mavis herself had named after a storybook prince. However, as the party died down, Mavis, now having grown into a beautiful twenty-three-year-old woman, took Precht into her office for a private meeting about Fairy Tail's future as well as their own.
"You're giving reins over the guild to me?" Precht asked her in surprise. Once Mavis nodded for confirmation, Precht then asked. "Why?"
Mavis showed a small smile as she then said. "I think you've got the right mind and heart to lead Fairy Tail when I'm gone, Precht, and I do intend to leave on our guild's upcoming anniversary. I love our home and family, Precht, but after a long time of thinking, I have decided that I do not want Zeref to be alone anymore. Therefore, once I leave, I'll find the right group of degenerates to use Fairy Law's base form on and get the same curse he has."
Precht's eyes showed sadness, but he nonetheless smiled as he commented. "You care about the old fossil that much, huh?" Receiving only a nonchalant shrug, Precht sighed before looking Mavis in the eyes as he said. "I accept the position, Master, and I hope that someday you and Zeref can pass on from life together."
"As do I, Master Precht." Mavis replied with her own sad smile.
July 2, X784
In the eighty-eight years since Mavis left Fairy Tail in Precht's hands, the Dark Guild as a whole had prospered even further due in no small part to Master Precht Gaebolg raising up strong Wizards to act as leaders in their own right to recruit more members and manage them one branch at a time. Among the branch heads, Jose Porla, who was in fact descended from the late Master of Blue Skull, Geoffrey himself, was known to be an ambitious and prideful man that not so secretly desired Precht's position for himself, but so long as he did his job, the long lived Precht was comfortable to let him be for the moment.
While the past eighty-eight years were not without their pitfalls such as the passing of Makarov's parents and the less frequent meetings with and messages from Mavis, Fairy Tail moved forward still with the confidence and strength comparable to an army with Makarov, his son Ivan, the still living Warrod, and Zeref's recommended Etherious among others making sure that money continued to roll in, the guild's reputation remained fearsome as ever, and every member was well taken care of. Fairy Tail's Guild Building, as a result of almost a hundred years of devotion, was by then, the tallest, most well-defended, and most luxurious-looking place in a Magnolia Town that had expanded along with it as Precht could see from the top of the building itself.
Seeing the diminutive, but no less strong, Makarov approach the Guild Master, Precht turned fully towards him as the former told him. "Apologies for the bother, Master, but I just wanted to let you know that I sent Natsu and his group to Hargeon to send the final debt warning to Bora not too long ago."
The far elderly Precht showed a small smile towards his almost as old student as he replied. "Very good, old friend. Let me know when our dear Dragon Slayer has something to report."
In Hargeon, Natsu Dragneel, his girlfriend, Mirajane Strauss, and their associated cat creature for a partner, Happy, had arrived to check on a down on his luck scam artist for a Wizard named Bora that owed Fairy Tail money for both extortionist and gambling reasons, and seeing how Natsu had to ride a train to get to Hargeon, he was in no mood for games. For Bora, it was either pay up or else, and Natsu said that to him in fact when the three arrived at his yacht.
Responding to their harsh glares with a gulp, Bora held his hands up for calm in an attempt to relax his guests as much as himself and his goons as he then explained how he was going to pay Fairy Tail back. "Simply put, Salamander, I've been pulling a good enough long con in the Fiore capital, Crocus, from Charming the local women there to setting up trade contacts in Bosco, so just give me tonight and your guild will have all the money I owe you and then some."
Unfortunately for the smug sounding Bora, he did not expect Natsu's fists to ignite in flames or Mirajane to transform with her Satan Soul Magic as they did so and approached him and his hired helpers threateningly.
"I'll be outside if you guys need me." Happy told Natsu and Mirajane in amusement as he made his way off the yacht.
A little while later, Happy saw the yacht explode from the inside-out as Natsu and Mirajane flew out and landed not so far from Happy who saw that the latter was holding a shapely blonde girl around their age in her arms.
"Who's that, Mira?" Happy asked in confusion.
The nicknamed Mira smirked as she cancelled her transformation and laid the intimidated blonde down. "Turns out that Bora not only landed on an actual gold mine in the form of the Heartfilia Konzern's heirless but was keeping her to himself."
"He kidnapped a rich girl?" Happy said in slight surprise that Bora was more competent than they gave him credit for.
Natsu merely shrugged as he explained. "Eh, she was already running away from home for over a year, anyway, but that's beside the point."
"Are you guys Fairy Tail members?" The blonde forced herself to ask them.
"What is it if we are, rich kid?" Mira asked in kind, eye to eye.
"My name is Lucy." The blonde retorted before adding resolutely. "And I want to join you."
Fairy Tail Guildhall, Magnolia Town, Later at Night
Arriving at Magnolia after another train ride, Natsu, Mira, and Happy gave the prospective member, Lucy, a brief tour of the town itself before heading straight for the guildhall of Fairy Tail. Although both Natsu and Mira were initially uncertain of Lucy's motivations at first, after the latter went into detail of how she felt unloved by her father and admired Fairy Tail's power and freedom, they decided to give her the benefit of the doubt, especially after she reacted positively to Natsu's comment of potentially stealing money from Jude Heartfilia through her.
"I'd love to see the look on his face when that happens." Is what she said at the time.
Entering Fairy Tail's Headquarters, Lucy found numerous guild members drinking on one end and arm-wrestling on the other. Letting Natsu and Mira handle introductions, she met Natsu's rival, Gray Fullbuster, being tended on by a lovestruck woman named Juvia Lockser who ignored the jealous advances of Lyon Vastia as Ultear Milkovich and Meredy rolled their eyes at the whole scene, the local disciplinarian, Erza Scarlet, sharing food with her childhood friends with Lucy recognizing one of them as the handsome Jellal Fernandes and another as a fellow Celestial Spirit Wizard alongside her younger sister, Mira's younger siblings, Elfman and Lisanna, two heavy drinkers named Cana Alberona and Bacchus Groh, and even met the famed Celestial Spirit Wizard, Karen Lilica, who she couldn't help but embarrassingly ask for her autograph.
It was then, however, that a small group of unusual people that Mira told Lucy were members of the Demonic Etherious race created by the infamous Black Wizard Zeref himself entered the building. Although Lucy could not help but feel intimidated by them, she was soon surprised beyond belief when Natsu approached them with a smile which they reciprocated before bowing in submission. Turning to Mira for explanation, all Lucy saw was a dubiously innocent smile before she walked up to link up arms with Natsu affectionately before Mira then turned back to Lucy and said. "Us Demons have to stick together, after all."
"So she says." Happy could not help but sing out as Natsu and Mira kissed each other with Lucy standing there in confusion.
Got the idea from the very first chapter of The What If Anthology on FanFictionNet by snakeboy33 mixed with a story also written by that author, Emperor of Sirius, but with some additions from Quatro Cerberus, Blue Pegasus, Phantom Lord, Grimoire Heart, and Raven Tail (because I figured that if Fairy Tail was dark, they would have taken a similar branch approach as Phantom Lord did, especially since the previous guilds are confirmed to have been founded either by onetime members of Fairy Tail or as a direct result of Fairy Tail's existence in Phantom Lord's case) combined with a few extras from the Tower of Heaven, Tartaros, and otherwise, and I did what I could to write it naturally rather than in a Crime Syndicate of America from DC Comics kind of way which, while not necessarily bad, wouldn't feel complete without the Legal Fairy Tail Guild to compare like how there's no DC Crime Syndicate without it's Justice League. I honestly would not mind adapting the core of this to my future full-length Dark Guild Natsu story in addition to another depiction of Mavis as an older woman as shown in the third volume of the Fairy Girls spin-off, but I am not completely certain on some aspects, so we will see how either of those go.
Also, to the moderators of the Fairy Tail Rare Pairs collection on Archive of Our Own where I have submitted a good amount of my Fairy Tail work towards, is there a reason why you haven't accepted Lies and Concerns as well as Enchanted Companions into it? Because I thought Natsu/Lisanna and Natsu/Erza/Irene/Juliet/Heine respectively were not common ships on there.
Lastly, I am sorry that it took so long to post this. Kept getting distracted one way or another.