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 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!

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.

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.

The coalition of conjurers gathers at their meeting place to discuss their plan to stop Oracion Seis. But when the allies are ambushed, the crew get a taste of the evil prowess they're up against!

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.

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.

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.

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.

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.

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."