預言斷定露西將逢致命遭遇，而一名記者則採訪妖精尾巴公會。

茱比亞決定用藥水引誘格雷，讓公會陷入一片混亂。

露西終於發掘初尾隨她一段時日的神祕跟蹤狂，究竟是何方神聖。

青色天馬、蛇姬之鱗、妖精尾巴和妖貓之宿四大公會聯手出擊，力圖擊潰六魔將軍這闇黑公會。

公會聯軍試圖擬定對策，不料六魔將軍先行現身。

擁有神奇治癒魔法的溫蒂，遭六魔將軍擄獲。公會聯軍試圖釋放溫蒂，以解救遭眼鏡蛇下毒的艾爾莎。

當公會聯軍與六魔將軍成員展開激戰，六魔將軍首腦命令溫蒂讓傑拉爾死而復生。

納茲幫助溫蒂和哈比，利昂則加入格雷行列，向雷射遞下戰帖。

溫蒂治癒艾爾莎，而涅槃則將光明逆轉為黑暗，魔法因此啟動。

露西、納茲和希彼基正在為阻止涅槃而準備時，卻被迫面對另一星靈「天使」。

傑拉爾迎面承受涅槃的首波魔法攻擊，並再次對戰艾爾莎。

首腦掌控涅槃之後，公會聯軍試圖趕往此移動城市高處，力求阻止首腦達成目的。

納茲和哈比決定殺死首腦，但兩人必須得先力抗眼鏡蛇。

首腦攻擊納茲，試圖將他納入六魔將軍旗下。裘拉決心弄清首腦目的，因此向他投下戰帖。

聯軍試圖阻擋涅槃，而艾爾莎和傑拉爾則需力抗午夜。

艾爾莎與午夜交戰進入尾聲，揭露首腦的裡人格：無，亦即六魔將軍公會的主謀。

涅槃即將毀滅妖貓之宿公會時，青色天馬的飛艇克里斯汀娜重現眼前。

納茲決意對抗無後，面對記憶逐漸恢復的傑拉爾。

納茲釋放滅龍魔法與無激戰。同時，大夥都準備好對付六個魔水晶。

傑拉爾向眾人道別，我們的英雄們前往妖貓之宿，會長羅鮑魯對大家娓娓道來公會最初創立的緣由。

溫蒂為第一份工作尋覓搭檔。同時，納茲得知附近曾有人目擊名為伊格尼爾的巨龍。

艾爾莎被一名陌生對手困惑。同時納茲與格雷對戰。

艾爾莎奮力阻止達芙妮的人造龍飛往木蘭花鎮，瓦卡巴和馬卡歐則試圖帶格雷回到公會。

馬卡羅夫命令公會與人造龍奮戰，而艾爾莎和格雷力圖營救納茲。

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.