After Universe One is dispelled due to Irene's death, Zeref sits in the Fairy Tail guild hall until he is approached by Gray. This surprises Zeref as he tells Gray that he thought either Laxus or Jellal would be the first one to reach him. Zeref then says to Gray that he put himself in a situation that will cause Natsu the most grief. and proceeds to reveal information about Gray as well as his other friends. Gray says that Zeref knows a lot about him and his friends, and they hardly know anything about Zeref. He questions Zeref's true motive, to which the Black Mage responds that he wants Fairy Heart to defeat Acnologia, but his real ambitions are not nearly as small as that.
After revealing his true purpose to a shocked Gray, Zeref lets Gray know that Natsu is on his way to the guild hall as they speak and when he finds Gray dead on the floor, it will anger him enough to fight Zeref at his full strength. Gray then tells Zeref that he knows that if Zeref dies, then Natsu will die as well. However, Gray says that even if Natsu is E.N.D., he is still his friend and proceeds with his trump card, getting into the Iced Shell stance. Zeref is shocked when he senses that the spell has a lost attribute in it and Gray reveals that when he uses the spell to seal Zeref away, it will erase Gray's existence from all of his friends' memories so that no one will be sad about his loss.
With Gray's Lost Iced Shell in the process, Zeref wonders how Gray could have applied a lost attribute into his spell. Gray tells him that when he was with Avatar, he learned a lot of things. As ice begins to form around Zeref, he tells Gray that the spell will only seal him away, and one day the ice will melt so that he can be free again. Gray understands this, but says that the world will be at peace until then, and Fairy Tail will emerge victorious. Suddenly, Natsu bursts into the guild hall, pushing Gray to the ground, and burning all of the ice in the guild hall. Natsu then tells Gray that he stopped him from using the spell before, while Gray responds by saying that he let his emotions get the better of him, and admits that he tried to kill Natsu. Tearing up, Natsu then shouts that he did the exact same thing as Gray and asks if Gray is still his friend, as Lucy and Happy enter the guild hall. Zeref then tells Natsu that it is his destiny to die, whether he wins or loses. However, Natsu shouts that he will not die and says that he will burn down his destiny. Zeref tells Natsu that it is impossible, and that he has already accepted his cursed destiny as he had no other choice. As the Black Mage takes off his robes, he and Natsu stare at each other.
Natsu and Zeref begin their second clash as Lucy, Gray, and Happy look on. The two brothers exchange blows, with Natsu pushing Zeref to the ground, and attempting to hit Zeref, only for the Black Wizard to avoid the attack. Zeref tries to punch Natsu, which the Fire Mage avoids. Natsu then sends a barrage of fire attacks at Zeref, who blocks all but one, sending him flying into a wall. Zeref quickly stands up and runs over to Natsu, avoiding his little brother's kicks and punches. Zeref then kicks Natsu into some nearby tables, which causes Natsu to comment that the attack hurt, while Zeref says that without Igneel's power, Natsu can no longer defeat him. Natsu tells Zeref that he still has his own power as he stands back up. Suddenly, everyone in the guild hall senses the arrival of Acnologia. Zeref says that Irene bought him a lot of time, but it is now up. He tells Natsu that he can no longer play with him now and asks his brother to lay down his life for the sake of humanity.
Zeref then powers up his fist with Magic as he hits Natsu, who runs at Zeref and kicks him. Afterwards, Natsu uses Fire Dragon Roar on Zeref, who uses a shield of Dark Magic to block the attack. Natsu jumps at Zeref, trying to kick him, but Zeref blocks the attack with a circle of Dark Magic on his fist. Jumping back on the ground, the two combatants ram at each other. Meanwhile, Mavis telepathically tells Lucy, Gray, and Happy to leave the guild hall, just as Natsu and Zeref send rays of Fire and Dark Magic at each other. As the three of them leave, Natsu grabs Zeref's arm and hits him with Fire Magic, sending him into the ground. Zeref rolls on the ground for a second, before jumping up and landing away from Natsu. He tells Natsu that their battle is fun and says that unless he takes Natsu down right now, humanity has no future. Suddenly, Natsu begins to feel drowsy, shocking Zeref. Larcade enters the guild hall, using R.I.P. on Natsu and saying that he made it in time to save his father. Natsu begins to punch himself, trying to stay awake, while Larcade hurries Zeref, claiming that it is his chance to kill Natsu and freeing himself from his brothers curse. Zeref looks on at the scene, angry and blasts a hole through Larcade's chest, shocking Larcade and Natsu.
As Larcade falls to the ground, he asks Zeref why he did that. Zeref stomps on Larcade's chest as he tells him that he has no children, which causes Larcade to weep, as he tells Zeref that he is his son. Zeref denies this as he says that Larcade is nothing more than a Demon from the Book of Zeref. The Black Mage tells Larcade that he interfered in his battle with Natsu as he begins to kick and punch Larcade, much to Natsu's dismay. Turning back to his brother, Zeref then asks Natsu to continue their fight, while Larcade lies on the ground, crying.
Not taking Larcade's next attempts to call him a "father" well, Zeref charges his fist with Dark Magic, and as he states that he cannot even stand the sight to see him anymore, the Black Mage uses the Dark Magic to kill Larcade. Natsu confronts Zeref telling him that Larcade was his ally, which Zeref denies, saying Larcade was neither an ally nor a son, causing Natsu to punch Zeref, sending the Dark Mage flying through tables. Natsu tells Zeref that he proved that he had no children, as there is no father in the world who doesn't love his kid.
Zeref says that he tried his best to attain happiness, but because of his Curse, he killed everyone he loved and did not allow him to have a family or to have a happy life. This angers Natsu, who begins to stomp towards Zeref, telling him that it isn't about what he is allowed or not allowed to do, but that he must make his own happiness, as that is what family is about. Natsu proceeds to say that if Zeref keeps on insisting that he has no family, then the little brotherly bond that he and Natsu share ends there. Zeref then ponders that it is strange that there used to be a bond between them at all. Natsu tells him that that is what emotion is about, to which Zeref agrees, calling his little brother E.N.D. Natsu and Zeref then begin to power up their Magic. Natsu charges up his Fire Magic as he strikes Zeref, sending him flying backwards. Zeref begins to become more bloodthirsty as he tells Natsu to give him more and to destroy him, which in turn will kill Natsu as well. Natsu tells Zeref to start making more sense as Zeref calls him "E.N.D." again. Natsu then shouts, saying that he is Natsu, not E.N.D.
Later, as Natsu and Zeref pant, the Black Wizard asks his brother if that was all he could give him. Zeref proceeds to blast Natsu with Dark Magic saying that Natsu disappointed him as he thought Natsu was the only one who could destroy him. Natsu screams as the Magic begins to wrap itself all around him. However, Zeref says that it is all right, saying that he can go back to what he used to be with Fairy Heart. He reveals that he plans on using the spell Neo Eclipse to reset time to before he became immortal. A shocked Natsu realizes that Neo Eclipse was Zeref's true plan all along. Zeref tells Natsu that he will return to a normal human being and Acnologia will be killed, asking what better happy ending they could ask for. Natsu angrily questions the fate of his friends, to which Zeref replies by saying he doesn't know. Natsu shouts that all of them are struggling just trying to live in the world they are in now. Zeref ignores Natsu's statement and tells him that there are two keys to Neo Eclipse, saying one is Mavis, who he says will arrive in the guild hall soon, and the other is the Space Between Time. Zeref then tells Natsu that he has found the Space Between Time and that it is brimming with so much Time Magic, that it beggars the imagination. As Natsu continues to struggle out of Zeref's Dark Magic, Zeref proudly states that the Time Magic belongs to him and that he sealed it away. He says that he'll only open it when Neo Eclipse is ready.
Suddenly, Mavis enters the guild hall, saying that she'll stop him. Zeref smiles as he says that all of the pieces to Neo Eclipse are here. However, Natsu begins to burn away Zeref's Dark Magic as he enters Dragon Force.
A shocked Mavis watches as Natsu stares at Zeref, who tells him that Dragon Force will not help Natsu beat him, as he does not have the same power as Acnologia: to turn into a dragon. Natsu yells that he is human and will never be like Acnologia, saying that Igneel did not want him to. As Natsu charges up his fist to attack, Zeref corrects Natsu, saying that he is hardly human and calling him "E.N.D." again. Zeref then begins to charge his fist with Dark Magic as Natsu starts running at Zeref, trying to attack him and saying that his fire is going to take him down. Mavis suddenly steps in front of Zeref, telling Natsu to wait. This shocks both Natsu and Zeref, as the Fire Dragon Slayer asks Mavis what she is doing. Mavis tells him to give her a chance and to let her talk to Zeref. However, Zeref grabs Mavis's head and tells her to stop meddling with his fight with Natsu. Mavis tells Zeref to hear her out and says that she can save him and release him from his immortal life, which Zeref refuses to consider, telling her that it is impossible and that he has tried everything to end his life. Mavis questions Zeref's fear of of Acnologia, to which he replies that Acnologia is too powerful and that once he ends humanity, they will be left because they are immortals and will become his playthings for all eternity. Mavis tells Zeref that she has a method of ending that eternity, but Zeref ignores her, saying that he has one too and begins to extract Fairy Heart from Mavis to begin Neo Eclipse, causing Mavis to scream.
As Natsu runs to Zeref, yelling for him to stop, Zeref blows him back using his Magic. He then explains to Mavis that Neo Eclipse is a Magic that lets a person live their life over and that he is going to return to his original self, 400 years ago. As Natsu struggles to reach them, Zeref says that he will kill Acnologia before he becomes powerful along with Natsu and says that he is bidding farewell to the world they are in now. As Zeref finishes extracting Fairy Heart from Mavis, she sadly tells him that he can't erase this world because it is where she met him. Mavis falls to the ground, with Natsu shouting her name. Zeref then tells Natsu that she is not dead, but that he sucked all of the Magic out of her and that she cannot even stand up anymore. Natsu angrily stares at Zeref as the Black Wizard activates Fairy Heart, turning him into a god that surpasses time and space.
Witnessing all of this, Natsu decides to disregard Mavis' plan to talk to Zeref and says that he is going to obliterate him. As Zeref laughs at this notion, Natsu charges at his opponent, using Fire Dragon King's Demolition Fist, which destroys the majority of the guild hall. Thinking that he had destroyed Zeref, Natsu apologizes to Makarov, saying that he wrecked the guild again along with Zeref. Suddenly, the guild hall begins to put itself back together, with Zeref reforming as well. This shocks Natsu and Zeref explains that that is the power of Fairy Heart, a limitless, eternal power and that he controls space and time. Zeref suddenly pierces through Natsu's chest with his hand, saying that Fairy Heart is a power fit for the end of the world. As Natsu falls to the floor, mortally wounded, Zeref says that there is no need to apologize to Makarov, as he is dead. Natsu starts to tear up, while Zeref says that he hopes Natsu will meet Makarov in heaven. Zeref says goodbye to Natsu when his lifeless body hits the ground.
As Natsu and Mavis lie on the floor, Zeref says that the world is over and a new one is about to begin. He then uses the doors of Fairy Tail to become the gateway to the new world and connects the doors with the Space Between Time. The doors begin to glow as Zeref states that the moment he passes through the doors, world will begin to crumble away and the new world will begin to take place. He also says that Fairy Tail's doors have seen countless adventurers leave and return home, and now Fairy Tail's doors will be both the end and the beginning of worlds. As Zeref starts to step towards the doors, he says that he will retain his memories as they are and go back to redo his life and not make the same mistakes again. As Zeref gets closer to the doors, he offers his thanks to the world. However, he is freezes when he hears Natsu quoting Makarov by saying that when you leave the doors you make a vow to always come back. Zeref turns around and sees Natsu stand up with his wound completely gone.
Natsu angrily stares at Zeref, who realizes that Natsu's wound is gone and that the Book of E.N.D. is missing, as Lucy is rewriting the book concurrently. Zeref says that rewriting a demonic script should be impossible for a human and states that even if they do rewrite it, the human would be corrupted by the book and plunged into darkness. Natsu slowly begins to wobble towards Zeref, who says that even though his recovery is miraculous, the one rewriting the book will soon die. Natsu ignores this and thanks Lucy, Happy, and Gray. He remembers Erza stopping the fight between him and Gray and also her words and says that he realizes that it was Makarov talking through her. Realizing his own selfishness, he states that he remembers why he is fighting. Natsu then charges, with his Fire Magic, at Zeref, who easily catches his fist and punches him with Dark Magic, sending him flying backwards and landing on a table. Natus shoots fire at Zeref, who dispels it with his own Magic and blasts it at Natsu. Natsu jumps off the table, just as the table is struck by the Magic.
Afterwards, Natsu runs at Zeref and punches him with his fire. Zeref angrily stares at him until Natsu continuously hits Zeref with his punches. Zeref asks Natsu how much longer he must meddle until he is satisfied, just as Natsu punches him once again. Natsu replies that he will continue until everyone can smile and laugh again. Zeref charges his fist up with Magic and tells Natsu that that's the world he's trying to create and strikes him, sending Natsu stumbling backwards. Natsu says that he is only thinking about himself and that all he's doing is rejecting the world he's in. Zeref angrily replies that Natsu has not suffered the rejection of the world like he has and says that Natsu knows nothing. Suddenly, Natsu begins to power up, unleashing flames all around him and Zeref, in turn, charges up his Magic in his hand. They both attack each other at the same time, with Natsu using Fire Dragon King's Demolition Fist and Zeref using Dark Blast Inferno.
As they both scream each other's names, their fists collide, causing a huge explosion. While they hold their position, Zeref says that Natsu's fire is so hot that his own Magic is burning up and that Natsu is incinerating his own soul. Zeref wonders if that is the guild's flame, as Natsu continues to overwhelm Zeref, saying that his fire is a raging flame of emotions. His fist finally strikes Zeref, burning away all of his Magic and sending him flying into the ground, defeated. Natsu, whose arm is terribly burnt, pants as he stares at his brother. As Zeref lies on the ground, he realizes that he cannot move and says that this has never happened before. However, he also states that he can't die still and that he will be perfectly fine soon. Natsu asks Mavis, who stands up, if she can deal with Zeref now, which she agrees. Natsu says that he wants to see his friends and walks out of the guild hall, but not before he says goodbye to his big brother one final time.
Mavis slowly walks over towards Zeref, who says that Natsu is incredible but also naïve, as his wounds will be completely healed soon. Standing over Zeref, Mavis tells him that he hurt her friends and that she can never forgive him for doing that. She then says that she wants to help him to permanently leave the world. She suddenly sits by Zeref and says that he can rest now, which Zeref claims not to be possible. Mavis then says that the reason she died was because she did not love Zeref as much as he loved her, as Zeref tells her not to worry because no one has ever loved him before and that the emotions she felt towards him was pity, not love. Mavis denies this, saying it was the Curse's contradiction. She tells him that because he taught her Magic, she was able to save Magnolia and create Fairy Tail. She continues on saying that even though he helped her, he still hurt her friends and tried to use her to destroy Fairy Tail. She tells him that she hates and loves him at the same time and that it's because she is the only one who feels the same loneliness at him. Mavis then reveals that her strategy to defeat Zeref was to love him, which in turn will kill him. However, Mavis begins to sob as she tells Zeref that she doesn't want him to die and that she wants to be with him forever. Zeref smiles at this and says that the more love they both feel, the more lives they take and that the answer to his Curse was to be loved the entire time. Mavis begins to cry uncontrollably, saying that he can't die and that she hates him. She begins to hit Zeref, telling him to go ahead and die and telling him that she doesn't love him. Zeref begins to cry as well, saying that he is very happy and it is all because of Mavis. Their kiss then actives the Curse, which surrounds them in a bright light. Mavis tells Zeref to take her with him as they begin to fade away, to which Zeref responds that they will go together as they disappear. Mavis agrees with him, saying that they are dying in the heart of Fairy Tail. They both realize that there is only one power that even an immortal cannot overcome, which is the power of love.
Outside of the guild, members of Fairy Tail look around and wonder if the battle is finally over. Laxus, who is holding the body of Makarov, notices that his grandfather has opened his eyes. This causes everyone to smile and cry, while Makarov states that he had a strange dream and that a warm power of life flowed through him as he saw a barefoot girl and a boy in black walk through a field of flowers together, smiling and holding hands.