ARC 1: THE DEATH OF FIORE.
Fairy Tail awakens after seven years in stasis, having thought themselves killed by Acnologia, and finds a world covered in darkness ruled by the TWILIGHT EMPIRE. Its Emperor, Zeref, after attaining the almighty power from FAIRY HEART, has expanded his reign from Alikitasia to Fiore, Stella, and has completely wiped the nation of Bosco off the map. To do this, he created five military divisions: THE DRAGON DIVISION, THE CRYSTAL DIVISION, THE HUNTER'S DIVISION, THE TARTAROS DIVISION, and THE TWILIGHT DIVISION.
They are rescued from the clutches of Minerva Orland, a General in the Twilight Division, by Hisui, the former princess of Fiore and a Celestial Spirit warrior, along with Mest. After more near misses and captures, they also meet Tayaka, who has taken up Ultear's power after she fell in combat trying to save Fairy Tail and Magnolia. The town has been destroyed, and the only survivors of Fairy Tail are Max, Laki, Porlyusica, and Romeo.
ARC 2: GRAND MAGIC GAMES
Fairy Tail gets on the move soon after Hisui leaves them to wreak havoc. Mirajane, Levy, and Lisanna Strauss, in an errand to find aid, get captured and are enslaved at an airfield showing great promise for improving the Empire's wealth. Though they are able to free the slaves and Mirajane defeats a demon of Tartaros, she is captured by Mard Geer.
The Dreyar family and Thunder Tribe go out in search of Bob of Blue Pegasus, who is still alive. In doing so, they are swiftly hunted by the Garou Knights and Jacob Lessio, Captain of the Hunter's Division. They manage to dupe him and capture him at Blue Pegasus's former guild hall, now a stronghold for the rebellion.
Fairy Tail's Strongest Team, alongside Elfman, Juvia, Gajeel, and Lily, head out to the Grand Magic Games, a new iteration of the event as it is now headed by the Dragon Division. Along the way, they meet Frosch, another Exceed, who is looking for his friend, Lector. Once they arrive where the games are held, in Clover Town, they are met by Axel, a Second Generation Dragon Slayer who reveals God Serena is dead and the lacrima he used have been distributed to incredibly powerful soldiers who proved themselves in the Grand Magic Games previously.
Fairy Tail rises to the top, while inadvertently supporting the ambition of Meredy and Kagura, members of the rebel group Crime Sorciere, and Erza devises a plan with Lucy to get in close with Axel, who is deeply infatuated with her, and secure information. Natsu defeats Axel, embarrassing him and prompting Sting to send an army after Fairy Tail. Meanwhile, Sting's wife, Yukino, sees through the execution of Jiemma Orland, a noted rebel, and begins to lose faith in the Empire as a whole, despite Sting's position and insistence they are doing the right thing.
Fairy Tail can barely stand to fight the full-on force, after their exhaustion from the games, and Lucy gives herself over to Axel so that her friends may live. Natsu and Erza are called to compete in the capital to see who will win that year's Grand Magic Games, and Fairy Tail sets out to rescue Lucy while they cause a distraction.
ARC 3: FIRE AND ICE, LIGHT AND SHADOW
Yukino's crisis of faith continues even as they get home, and her sister, Sorano, believes she just needs to lighten up. After attempting and failing to get the spark of romance back with Sting, Yukino closely observes rebel activity.
On the run from the airfield, Levy, Lisanna, and former Magic Council Custody Enforcement Unit leader Lahar are ambushed by the Wizard King, AUGUST. There, Levy is shown the gruesome deaths of her friends at Mirajane's demonic hand and agrees to leave with him to save their lives.
Lucy hates living with Axel, who hounds her for intimacy. She is introduced to the Twilight Division, the most powerful wizards in the Empire, who take interest in her complimenting Yukino's Celestial Spirit powers. Lucy is also reintroduced to her father, who is a close ally of both the Empire and rebellion, having turned himself around in the seven years since Lucy's disappearance.
On the road to Crocus, Natsu and the others run into Kip, a handless beggar looking for entry into Crocus. Kip shows good skill with earth-based magic. Natsu and Erza are picked up by Invel the WINTER GENERAL to fight in the games. Kip manages to burrow them into the DRAGON GRAVEYARD, where they are found by Gale Dragon Slayer Johan. Kip, backed into a corner, reveals he is the Empire's Cavern Dragon Slayer and helps them defeat Johan, declaring himself an ally of Fairy Tail as he is from Bosco, which was destroyed, and wants revenge for his people.
Minerva, all this time, finds herself bored with the Empire. Seeing as how the Hunter's Division captain is effectively missing and presumed dead, she begins her campaign to ascend to that height by trying to assassinate Rufus, a former ally of hers and one that is of great use to the rebellion. She leaves a trail of blood and fire in her wake and successfully kills her old colleague with no remorse.
Yukino witnesses Jiemma's turn to a demon of Tartaros, the same as Mirajane's, and feels ambivalent toward the Empire gaining such a tough ally. Natsu and Erza fight and Erza wins, throwing Natsu in prison. Yukino visits him, Sorano, and Sting, and comes to the conclusion that she is no longer fit to be an Imperial, and wishes the world to return to how it was. She abandons Sting, who reveals his desperate need for not her but her power at this time, which infuriates him, and he pins all the blame on Natsu.
Fairy Tail and the Empire finally come to blows as Kip attacks the prison at the same time Sting and Rogue arrive. Natsu finds Lucy but she convinces him to go on without her, as she can do good for Hisui in attempting to undermine the Empire from within a relationship with Axel. On their way out, Natsu and Gray fight Sting and Rogue to the brink, while Gajeel, Wendy, Erza, Elfman, and Juvia charge on. Erza and Elfman take on Mirajane while the others get to the city's main gate, and are helped by Yukino, who then flies in to get Natsu and Gray away, revealing herself as a traitor to the Empire at last.
Kip stays behind and meets Lucy, informing her he is on her side, while Lucy and Levy affirm their friendship in the face of the Empire's might.
Meanwhile, Sonya, the former queen of Stella and current Empress as a result of a marriage pact formed with Zeref when the Empire invaded her kingdom, wakes from a year-long slumber and finds that her rule has been nearly undermined entirely by August. She begins to claw back some power while fending off Animus, the dragon soul living within her. She cannot remember why she fell asleep, nor where Zeref is, as he is most certainly missing without a trace.
ARC 4: FAMILY
In the wake of their embarrassment, Sting and Rogue are cast down and out from the Empire, letting Zash Cain, the Purgatory Dragon Slayer and one who found the Dragon Cry weapon, take command. Minerva is not made Hunter's Division captain, incensing her. Sorano begins to have similar doubts about the Empire but feels she has some sort of domineering ability over it and decides to stick around, though is riding that line loosely.
Gathering back together and training for a couple of weeks, Fairy Tail once more branches off to separate paths: the Dreyars and Thunder Tribe are going to seek out Gildarts and other friends of Makarov, while he sends Tayaka, Cana, Romeo, Max, Laki, Lisanna, Elfman, and new ally Flare Corona (who has begun an unofficial flirtation with Lisanna) to find and train with Gildarts in the countryside. Natsu's team and Juvia, at Erza's urging, are going out to find Jellal, while Gajeel and Lily want to go find the Exceed Village that escaped from Edolas and check in on them.
All the while, the Empire begins their next move, which is countered by Meredy and Hisui: minor dark wizards begin springing up and poking at various rebel bases around the country, prompting the two rebels to wonder what this gambit is all about. Kagura is dispatched to get Frosch and Lector to the Exceed village safely. Sting and Rogue are en route to find the two Exceeds.
Makarov's crew are quickly distracted by the arrival of his son, Ivan Dreyar, who, they come to learn, is working with Dimaria Yesta, who is toying with them to bide time for a confrontation with Laxus and Makarov. Along the way, they scorn Ivan for his wretched behavior, particularly when he reveals he was the one who led Zeref to Fairy Heart and allowed him to assume ultimate power. They find Dimaria in the ruins of Magnolia, and despite a hard-fought battle, Laxus isn't nearly enough to take on Dimaria. Ivan sacrifices himself to get Laxus and the others away.
Natsu and the others are ambushed by Minerva and other hunters, including (unknowingly), the brainwashed and soul-wretched Bisca and Warren, and only escape thanks to the timely arrival of Mystogan. The King tells them that he and Jellal have swapped, thanks to an opening of an anima gate over the Tower of Heaven. Mystogan can open it once more, and the team sets out to Edolas in search of Jellal. Along the way, they meet a curious woman, IRENE, who joins them, much to Yukino's dismay as she is one of the greatest wizards in the Empire's arsenal. Eventually, they do locate Jellal, who'd been defending the Fairy Tail guild from surprise Imperial warriors for over a year, along with meditating and finding himself. At first unsuccessful, the group does manage to get Jellal to come home with them in the nick of time to fight Minerva once more. Irene has also joined them, swearing not to join the fight but to only help Erza if she has to. Jellal is officially back in the rebellion, and in the fighting, Minerva is slain, and the Hunter's Division is wiped out.
Lucy gets orders from Hisui in the capital: find Lullaby, the demon of the Book of Zeref, and use it to wipe out as many as she can. While she studies to find it, she trains with Kip and Levy, attaining the power to use her Star Dresses as Yukino can. Axel proposes to her and she accepts, but holds off the wedding as long as she can, getting her dad's support in doing so. One day, she is kidnapped by Brandish of the Twilight Division. By midnight, she must hand over her keys.
At dinner that same night with Axel, he reveals there has been a traitor among Levy and Kip, and that he knows all about her Lullaby operation. After she hands her keys to Brandish, Axel will torment her and force children upon her. She will live as his slave forever.
Lucy walks with heavy feet to the tower and meets Brandish, who has given her the chance to see her father one last time. She begs Brandish to allow Aquarius to talk but Axel interrupts everything by killing Lucy's father. Lucy is saved from them by Kip, who helps Lucy get away from Brandish as Aquarius is still summoned to reveal the truth of what happened between Lucy and Brandish's families so long ago.
Lucy fights Axel but is unable to secure a victory. Kip gets Lucy away and Axel shoots a diamond through Kip's heart. Almost free, Lucy is found by Levy and August, who has Lullaby. August tries to get Levy to use it on Lucy but Levy resists, destroying the weapon and gets seemingly vaporized in the process. Out of respect for learning the truth, Brandish prevents August from killing Lucy and allows Lucy to escape. Lucy believes both Levy and Kip are dead, along with her father.
Gajeel and Lily defend the Exceeds from a band of Dark Wizards when, a few days later, Sting and Rogue show up just after Kagura, Frosch, and Lector. The two Exceeds refuse to go back with their old friends, citing their behavior as Imperials. Said Imperials paved the perfect path for Zash to find the Exceed village, as well as Gajeel and Kagura, and brought the full might of the Fourth Generation Dragon Slayer army upon it. Gajeel and Zash begin to fight when five other Second Generation Dragon Slayers join the fray. On death's door, dozens of Exceed warriors take up arms and defend Gajeel, including the Queen, who is killed. Gajeel manages to consume some iron that is burning with Zash's flames and assumes a Purgatory Iron Dragon Slayer mode that overwhelms his foes. Kagura accidentally maims Sting and Rogue, who decide to fight against the Empire, en route to eliminating the army, and the Dragon Division is eradicated down to only three members. The Imperial Dragon Slayer lacrimas are destroyed, and Sting and Rogue leave with Frosch and Lector to heal, mentally and physically.
Everyone reunites some days later, discovering what happened all around, but are at last, at least, back together. Irene decides to inform Erza that one year ago, Zeref went off to have a confrontation with Acnologi, and neither ever returned. At the same time, Sonya awakens from a dream where she is there, at that confrontation, and knows she is the last person to have seen either of them alive.