In the land of Fiore, magic is everywhere. Sorcerers are like skilled tradesmen who band together in "guilds" and take on paying assignments for non-magic wielders, like hunting monsters, retrieving lost items or running odd errands.
Lucy is an aspiring wizard who wants to hook up with the coolest guild around, Fairy Tail. One day, she meets a red-headed boy who saves her from a unscrupulous wizard, and before she knows it, she's introduced to the wild and wacky band of wizards of Fairy Tail and begins the adventure of a lifetime.
A reporter from "The Weekly Sorcerer" comes to interview Fairy Tail. Cana tells Lucy that she will have a fateful encounter.
Love is in the air as Lucy thinks that Natsu has secret feelings for her. Meanwhile the whole Fairy Tail guild is turned upside down because Juvia whom believes that her relationship is going no where employs magical help from a love potion which in fact turns out to be a potion which makes the person who drinks it think that the first thing they see is their rival; Juvia attempts to use in on Gray but misses multiple times making everyone in the guild have rivals.
Someone has been following Lucy for a while and takes caution. She finds out that her stalker is none other than her father, who narrates that Heartfilia Railways has been confiscated. He tells that he went to Lucy to ask for 100,000 jewel but she refuses. When Lucy is about to decide on a job, she overhears the other guild members discussing about a place called Acalypha, where a trade guild, Love and Lucky, is being held up by a group of armed robbers. Lucy recalls that her father had mentioned deciding to go work at a trade guild in Acalypha, which leaves her worried. She arrives there, in hopes of saving her father. With the help of her celestial spirits, she saves the victims from the robbers, but is surprised to find out that her father was not one of the victims, and only arrived after the victims were saved, since he had to walk. Lucy's father apologizes to Lucy, regretting what he had said the previous day, regarding asking Lucy for money.
Fairy Tail is joining up with other guilds - Blue Pegasus, Lamia Scale and Caitshelter - to defeat a dark guild named Oración Seis. These four guilds will each send out members to strike the six members of the Oración Seis down. From Fairy Tail, Natsu, Lucy, Gray and Erza are chosen. They are sent to Master Bob's villa (from Blue Pegasus) to meet up with other members of other guilds. They first meet the representatives of Blue Pegasus, the Trimens - Hibiki, Eve and Ren - and Ichiya. Afterwards, they meet Lyon and Shelly, whom they fought with before, and Jura from Lamia Scale. The episode ends with everyone surprised upon seeing Wendy from Caitshelter, a petite girl who arrives last.
Wendy makes her entrance, but she's not alone. Her cat, Charle, has arrived with her, much to Happy's pleasure. The members of Blue Pegasus explain that the Oración Seis were after an extremely powerful spell sealed in Worth Woodsea - The Nirvana. The team of twelve (not counting the cats) go through a plan, whereby they take down the base of the Oracion Seis with Blue Pegasus' pride and Joy - a magical bomber, Christina, the Pegasus. Lucy and Wendy are worried about taking down the Oración Seis, consisting of Cobra, Racer, Hot Eye of The Heavenly Eye, Angel, Midnight and Brain. After discussing the plan, the excited Natsu runs off by himself, eager to defeat Oracion Seis on his own. Everyone else follows, unaware that Jura and Ichiya have already been beaten by Angel. The Oración Seis, with Angel's help, now know the plan of the joined guilds. Everyone else reaches the Worth Woodsea, only to witness Christina being taken down! Oración Seis appears, and easily defeats everyone but Wendy, who chooses to hide behind a rock in fear. Just as Brain is about to use a spell, he stops, having seen Wendy.
Wendy is captured by the Oración Seis, and so is Happy! Erza is poisoned, and the poison is spreading through her body, which will eventually lead to her death. Erza requests for her arm to be cut off, but Charle says that Wendy can save her. Turns out, Wendy is the Sky Dragon Slayer, who has healing powers. The representatives intend to save Wendy and Happy, in order to be able to heal Erza. Oracion Seis intend to use Wendy's healing power to resurrect a certain person. Lucy stays behind with Hibiki to take care of Erza, while the others set off to rescue Happy and Wendy. On the way, Natsu, Gray and Charles are surrounded by Naked Mummy, who is working for the Oracion Seis, and have to defeat them. Wendy is ordered to revive a certain person, and that person is ... Jellal!
Natsu and Gray are up against the Naked Mummy guild. Meanwhile, Wendy is instructed to revive Jellal, who she "owes her life to". Wendy, though having heard of Jellal's bad deeds before, does not believe in them. Instead, she decides to resurrect Jellal, the one who saved her life. Natsu and Gray easily defeat the whole Naked Mummy guild, and are now up against Erigor, whom Natsu had once defeated. Lamia Scale and Blue Pegasus (excluding Hibiki and Ichiya, since Ichiya was captured) also defeat the other guilds they are up against. Nastu soon defeats Erigor, and everyone finds out where the base of Oración Seis is by asking those they defeated. Having reached near the base, Natsu shouts for Happy and Wendy, and attracts the attention of the Oracion Seis. Racer starts a fight with Natsu and Gray. Natsu and Charle go to find Wendy and Happy themselves, while Gray battles Racer alone. The two arrive to see Jellal revived. Natsu, Happy, Wendy and Charles leave first in order to heal Erza. Racer sees them escaping and tries to stop them, but Gray stops him in his tracks instead.
Hibiki manages to communicate with Natsu through his magic, Archive, and informs him how to get to where Erza is. Meanwhile, Gray is having trouble defeating Racer and his Dead Grand Prix, a ton of magic motorcycles. Gray gets on one of the motorcycles and starts a race battle with Racer. Halfway through the race, Gray encounters Lyon and Sherry, and Lyon joins in the battle. While in battle, Lyon discovers Racer's weakness and whispers it to Gray, and then freezes Gray. Sherry joins in too, but soon gets defeated. Lyon almost gets defeated, and when Racer is just about to stab him, he tells Racer that he knows of his magic - lowering the speed of his opponents, or rather, slowing down their sense of time in a certain area. Gray has broken free from the ice and is at the tip of it, and fires an ice arrow at Racer. However, Racer reveals an explosive lacrima on his body, and plans to take Gray, Lyon and Sherry along with him by killing them. Just as Racer is about to run to Gray, Lyon grabs Racer and jumps down the cliff, followed by a huge explosion. Brain knows that Racer is defeated, and wakes up Midnight.
Jura starts a battle with Hot Eye of the Heavenly Eye, and Wendy wakes up and heals Erza. Meanwhile, Cobra follows Jellal, being unable to read his mind, to see that Jellal finds Nirvana. Natsu runs off to find Jellal, determined to not let him meet Erza. Erza hears the name "Jellal" and sets off by herself without the others knowing. Racer's personal guild, Harpyia, tries to stop Natsu, but is easily defeated. Hibiki explains about the power of Nirvana - the people in between the power of light and darkness switch to the opposite element. The people of light who feel powerful negative emotion fall into darkness. Fearing that Wendy, who blames herself for reviving Jellal, would fall into darkness as well, Hibiki knocks her unconcious. Meanwhile, Sherry, who feels that Gray has caused Lyon's death, has fallen into darkness, and knocks Gray unconscious. Hot Eye is also affected by Nirvana, and teams up with Jura. Ren heads toward the light, but Midnight, who begins to hunt the magicians, gets Eve as his first victim.
Natsu is after Erza and Jellal and Lucy and Hibiki and Carla and Wendy are after him. As they search for him Natsu appears to find Gray unconsious in a stream. Natsu helps him out but Gray is actually two spirits from Oracien Seis. Gemi and Mini twin spirits of Gemini. They can copy anyone and know exactly what their thoughts are and copy their magical power. Gray (Gemini) undoes and anchor on a raft which Natsu is on and Natsu becomes sea-sick. Lucy and Hibiki arrive and see Gray is about to kill Natsu. They assume he has fallen for the darkness of Nirvanna. When they try to stop him Gemini takes on the form of Lucy then is able to control Saggitarius, who Lucy called out to stop Gray, Saggitaruis shoots at Hibiki making him unable to battle. Then Oracien Seis's Celestial Spirit Wizard appears, Angel. She tells Gemini to stop. Lucy replaces Saggitarius with Aquarius and Angel calls out Scorpio. Lucy does not know Spirit relationships like Angel and Angel knows Scorpio is Aquarius's boyfriend. They go off together leaving Lucy's powerful spirit unusable. Then Lucy calls out Leo (Loke or Loki) and Angel calls out Aries. Angel proclaims she killed Karen and Hibiki becomes enraged. He mutters that Angel killed his beloved, he begins to fall into darkness. Although they love each other Aries and Leo begin to fight and Lucy is unable to watch. Angel proclaiming that Leo is more powerful than Aries she calls out Caelum and tells it to shoot at Aries and Leo together. Lucy becomes upset at how Angel treats her spirits and asks Angel to release Areis from her contract, to let Leo and Aries to be together. Angel tells Gemini to kill Lucy in order to release Aries. As Gemini starts they hear Lucy;s inner voice. They are moved by how she loves Spirits through her thoughts. They claimed they couldn't kill someone who loves Spirits so much. Angel closes the gate and Hibiki, who is close to falling into darkness, gives Lucy a powerful spell to save him from falling into the darkness, Urano Metorea. Lucy uses it to defeat Angel.
Though Angel is defeated, Lucy and Natsu end up falling down a giant waterfall; when they regain consciousness, they are attacked by Sherry, who is stopped by Gray and Lyon. Wendy reveals to Charle her past concerning Jellal and how she came to Cait Shelter. Meanwhile, Erza finds an amnesiac Jellal at the site of Nirvana; Jellal reveals that he placed a self-destructive spell on Nirvana, which Oración Seis mage Cobra is unable to dispel. Seeing the pain he has caused Erza, Jellal places a self-destructive magic upon himself.
Brain manages to gain control of Nirvana and actives its second stage - a monster that begins marching towards Cait Shelter, causing Natsu, Gray, Lucy, and Happy to rush off and defeat it. When Natsu and Happy try to get ahead, they are forced into an aerial battle against Cobra. Meanwhile, Erza saves Jellal and convinces him to live for the future, and they begin to devise a plan to destroy Nirvana.
Because Cobra can predict all his moves, Natsu can't gain the upper hand until he fights instinctively. When Cobra uses his new generation "poison" dragon slayer magic, Natsu loses his mobility, but wins the battle with a deafening roar.
Jura displays his true power and shows why he is one of the ten wizard saints. He battles with Brain, the leader of Oracion Seis and in a short battle defeats him. On the other hand Hot-Eye is winning his battle against Midnight and soon completely beats him. As Brain is about to fall unconcious, he thinks about his prayer - that Midnight should never disappear. And with that Midnight is shown to be revived and then crushes Hot-Eye in an instant saying that magic doesn't affect him. Natsu and the others wonder how they will be able to stop Nirvana from moving towards Cait Shelter.
Midnight fights a battle with Erza and Jellal; being weakened from the destruction magic, Jellal loses the fight easily. After initially being overwhelmed, Erza figures out the true form of Midnight's magic and prepares to fight him again. Meanwhile, Wendy searches for Jellal in order to find the necessary information that will help Natsu and the others stop Nirvana.
Erza manages to overcome Midnight's illusory magic, while Natsu, Gray, Lucy and Happy confront Brain's staff, Klodoa. Realizing Midnight's defeat, Klodoa explains that Brain has an alternate destructive personality called Zero that was kept sealed by the members of the Oración Seis using body link magic. The seal is released and Zero emerges and defeats Natsu, Grey, Lucy and Happy with ease. Erza, Jellal, Wendy and Charle make haste as Zero initiates Nirvana to fire upon Cait Shelter.
As Zero fires on Nirvana, Blue Pegasus's ship Christina, held together by Lyon, Sherry, and Ren, destroy one of Nirvana's legs and cause it to miss. Hibiki relays the details of the plan to stop Nirvana: within 20 minutes, the six legs of Nirvana must be destroyed at the same time. As Natsu goes to the location of first Lacrima to fight Zero, Jellal follows him after regaining some of his memory.
Having told Wendy to destroy the sixth Lacrima in his place, Jellal appears at the first Lacrima and gives Natsu the "Flame of Guilt". Natsu consumes the flame and enters Dragon Force for his fight against Zero and they power up for the final blow. Meanwhile, everyone reaches their respective destinations and wait for the right moment to strike.
As everyone gathers their strength for the final blow, Natsu is consumed by Zero's "Genesis Zero" attack. As he floats in the world of nothing, Igneel's voice speaks to him and he breaks free, defeating Zero and manages to destroy Nirvana's legs along with his allies, resulting in Nirvana's destruction.
Agents from the government dispatched to the site of Nirvana's fall arrest Jellal; while everyone else resists, Erza stops them and urges the officials to take Jellal away, though she is devastated by the outcome. As everyone recovers at Caitshelter, it is revealed that the entire guild was an illusion created by the spirit of its guild master for Wendy's sake. With Nirvana's destruction, the spirit has fulfilled its purpose and Caitshelter vanishes. As Wendy is left behind crying, Erza invites her to join Fairy Tail.
After saying goodbye to the Alliance the group returns to Fairy Tail, where Wendy and Carla get a warm welcome from their new guild. Erza encounters a mage with Requip magic similar to hers, while Gray tells Natsu that a woman named Daphne says that she met a dragon. When Natsu and Wendy go the Inn where she lives, they are caught in a trap arranged by Daphne. After trying to escape Gray suddenly comes in and challenges Natsu to their ultimate fight.
Gray and Natsu are fighting with all their power while everyone at Fairy Tail begin to worry. When Erza and Lucy decided to go and find their freinds, they encounter beasts that mimic their abilities. When Natsu is finally caught, Daphne reveals a handmade dragon designed to drain Natsu's power.
As Daphne sucks out Natsu's magical power, Erza is fighting copies of herself in different armors in monster form. Elfman, Wakaba, and Macao comes and battle their copies too. Natsu remembers a faint voice. He remembers how he promised a town to kill or defeat someone who controls dragons. Knowing that, he bursted a loud Roar. Gray was called to the master's room because he betrayed Fairy Tail. All of the fairy tail members help destroy the dragon as Natsu made his decision, he plans to die with the dragon.
While Natsu was still inside the artificial dragon, Fairy Tail had the dilemma whether to save Natsu or prevent Magnolia from being destroyed. Meanwhile, Master Makarov confronted Gray why he had betrayed Fairy Tail but Gray revealed his reasons for the act and Master Makarov gave him the plan to save both Natsu and Magnolia.
Team Natsu along Wendy and Charle are on a mission in the mountains. Because of the snow, Lucy catches a cold and she can’t go to Fairy Tail’s annual flower watching. Natsu doesn’t have fun because of this and he and Happy unroot one of the cherry trees so that Lucy can see it.
Wendy's gotten used to doing jobs at Fairy Tail and wants to try taking on something bigger so she can be more help to everyone, but gets into an argument with Carla over it.
The 24 hour race begins as all the Fairy Tail members race to get Wyvern Scales from the top of Mt. Ivor. There is no dropping out and no Flying Magic is allowed so Happy's in a difficult position but that does stop him from winning. Natsu,Jet Gray and Gajeel lose and have to do embarrasing photo spreads for the Weekly Sorcerer for two weeks as their punishment! And Happy is crushed by the fact that his prize is cheers of joy and the honor of winning.
Gildarts has finally come back to Fairy Tail after a hundred year quest and has news for Natsu concerning Igneel.
Wendy finally meets Mystogan, who she had known as Jellal in her childhood. He warns her about Anima, but as Wendy attempts to warn Fairy Tail about Magnolia's destruction, light shines down from the sky and the city disappears. Wendy finds that Natsu, Happy, Charle and herself are the only ones left.
Knowing that all Fairy Tail members have disappeared, Natsu, Happy, Wendy and Charle went to Edolas using the remaining traces of Anima. They finally got into Edolas, seeing a very different scenery. After a while, they finally found a Fairy Tail guild. However, what they found is not the same as they imagined it would be.
Natsu, Wendy, Happy and Carla are scared stiff at the Lucy of Edolas, until she mistakes Natsu for his Edolas counterpart and greets him -- with several grappling moves. Everyone is very different... but where's Erza? Why is THIS Fairy Tail on this run? And who's the Fairy Hunter?
After a narrow escape from Erza Knightwalker, Natsu's group decides to head to the capital of Edolas on their own to save their friends, despite warnings from the Edolas Fairy Tail. However, they soon find themselves guided by Lucy Ashley, Lucy's Edolas counterpart, and Natsu and Wendy are shocked to discover that their magic does not work in Edolas.
In the capital, Natsu and Wendy are surprised to find their Lucy alive and fully capable of using her magic. After Edolas Lucy and Earthland Lucy become acquainted with one another, Natsu's group escapes from the Royal Army and takes refuge in a hotel. When their plan to sneak aboard a Royal Army airship fails, they are saved by the timely arrival of the driver of a 4-wheeled vehicle - the Edolas version of Natsu.
Earthland Lucy, Natsu, Wendy, Charle, and Happy reach the Royal City, where they find a Lacrima made from the magical energy of Magnolia. To save their friends, Charle reveals that she has had information about Edolas flowing into her head since they arrived, and the group devises a plan based on getting close to the King of Edolas and having Lucy use Gemini to learn how to transform the Lacrima back. Their plan is foiled when they are ambushed by Erza Knightwalker, whose forces exalt Happy and Charle as beings known as "Exceeds."
Because Natsu and Wendy are Dragonslayers, they are locked up and wind up discovering a secret about the Exceed. Happy and Charle are brought to Extalia, the home of the Exceed, and learn the true reason why they were sent to Earthland in the first place. Meanwhile, Edolas Gajeel plans a distraction so Earthland Gajeel can attempt to destory the lacrima that holds his friends.
After hearing the truth about their mission, Happy and Charle run away from the kingdom and end up with two mysterious cats, Lucky and Marl, who's egg had been taken by the queen to be used in the Dragon's Slayer Extermination Project. And Happy and Charle's hearts have been shaken by the kingdom and by what they think they had done. Will Happy and Charle find strength within their own hearts to go save their friends? It is implied that Lucky and Marl are actually Happy's parents.
Happy and Charle rush back to the city to save their friends. Meanwhile, Lucy is imprisoned and she pleads Erza Knightwalker to let her go and save her friends. The Edolas Erza attempts to kill Lucy by dropping her from the tower with her spear. But Happy and Charles save Lucy from her fall. Charles finds out Natsu and Wendy's location. The magic-crazed King activates Code ETD (Exceed Total Destruction)on the Exceeds that were after Charles and Happy, turning them into lacrima. Erza ambushes the three of them, but Earthland Erza and Gray step in to save their comrades.
Gray, Lucy, and Charle went to rescue Natsu and Wendy while Earthland Erza hold off Erza Knightwalker. Happy went off to get Gajeel so he can rescue the rest of Fairy Tail members that has been turned into lacrima. In Edolas, Dragon Slayer power is capable of doing that. Apparently, the king is planning to use the floating lacrima as a bomb to destroy Extalia. After the Dragon Slayers' rescue, Wendy and Charle went to Extalia to warn the Exceeds about the danger that is about to be brought. While searching for the king, Natsu, Gray, and Lucy are intercepted by Hughes and Sugarboy. Meanwhile, Gajeel is being held off by Panther Lily.
Natsu,Gray and Lucy engage in battle to save there friends and the Exceeds from being destroyed against Royal Army Captains, Hughes and Sugarboy, and the Chief of Staff of the Royal Army of Edolas, Byro. Coco steals the key to the Dragon Chain Cannon, the weapon required to fuse the lacrima island with Extalia. While Lucy thought she was still chased by monsters she and Coco bumped each other. Coco thinks twice whether to give the key to Lucy or not. Byro chases after Coco, and tells her to give him the keys. To the confusion of Lucy,she thought he wanted her keys. She then engages in battle to Byro.
After Lucy calls multiple spirits in a row to fight Byro her magic is quickly drained, though Virgo gives Lucy a Spirit World whip that can extend and contract to help in the fight. When Byro is defeated by the timely arrival of Natsu, Coco gives the key to Lucy, but it is stolen by Sugarboy, forcing Gray to pursue him.
Gray defeats Sugarboy and destroys the key after learning its purpose, as he can create another key from ice. However, Erza Knightwalker captures both Gray and Natsu and brings them before the king, whom she quickly takes hostage, revealing herself as Erza Scarlet. Erza's plan to force the guards to redirect the cannon goes awry when the real Erza Knightwalker appears.
The queen of the Exceed reveals that her divine image was a lie perpetuated by the Elders to protect the Exceed from humans, but her inner strength convinces the Exceed to try and save Extalia with their own strength. When the lacrima suddenly disappears, Mystogan arrives to explain that he has restored Magnolia and thanks Panther Lily for saving his life while Lily reveals Mystogan is Prince Jellal of Edolas.
The Earthland wizards succeed in preventing Extalia's demise, but the battle is not over. Erza Knightwalker leads an ambushed by the Edolas Royal Army, while King Faust unleashes a super-powerful mechanical dragon, Dorma Anim. The Dragon Slayers confront the king, Erza Scarlet faces off against Knightwalker, the others battle the army while Mystogan and Pantherlily attend to other matters.
The battles against the Edolas Royal Kingdom rages on. The army, Knightwalker and the king himself are all fighting against the Earth Land Mages who wish to recover their friends. Meanwhile, Edolas Fairy Tail tries to come to a decision on which side they'll choose.
In the midst of the exhausting battle between the Edolas army and the members of Fairy Tail in both worlds, the Edolas combatants panic upon realizing their magic is disappearing thanks to Mystogan reversing Anima. However, to ensure the stability of Edolas, Mystogan declares himself a villain to Edolas and orders Pantherlily to kill him and emerge as a hero amongst the people.
Out of devotion, Pantherlily refuses to accept Mystogan's plan, but they soon find that Natsu, Wendy, and Gajeel have captured King Faust and begun a riot. When Mystogan confronts Natsu and defeats him, Mystogan is revealed to be the Prince of Edolas to the people. As the reversed Anima takes all the Earthland mages and the Exceed to Earth, everyone says their goodbyes while Mystogan remains behind, heralded as the new leader of Edolas.
On Earthland, the queen of the Exceed reveals that Exceed eggs had been sent to Earth to save them after she foresaw that Extalia would fall; Charle, possessing the same powers, had mistaken these visions as a mission. When the Exceed leave to find the remaining eggs, Panther Lily remains behind to be Gajeel's partner and to honour Mystogan's dedication to Fairy Tail. However, Panther Lily has brought them an unusual captive: Lisanna, who explains she is actually Earthland's Lisanna.
The aftermath of Natsu and his friends' adventures in Edolas is revealed: Edolas Fairy Tail moves closer to the kingdom to help rebuild the destroyed city, while Mystogan banishes the repentant Faust and sentences the remaining members of the Royal Army to assist with repairing the city. In Earthland, Lisanna returns to Earthland's Fairy Tail while Natsu and his friends tell the other guild members about their adventures in Edolas. Meanwhile, a young black-haired man is shown living in a forest where he causes all living things around him to die against his will, and says he wants to see Natsu.