After Irene's death and the dispelling of Universe One, Acnologia is able to return to the battlefield. He lands at Fairy Hills, where Erza and Wendy are, along with Irene's corpse. Acnologia announces that he is tired of the whole world and vows to destroy it. He then notices Irene's corpse and walks over to it, ignoring the two Fairy Tail Wizards. He identifies her as his mother as she was the one who created Dragon Slayer Magic. He then cruelly mutilates her corpse while cackling, shocking the two.
Erza shouts at him, telling him to stop and to not defile the dead. Acnologia turns and says that she bears a similar scent to Irene. He then notices Wendy and shockingly identifies her as a Dragon Slayer. Erza and Wendy both realize who he is at that point. Acnologia suddenly unleashes an attack at them, but it is blocked by Jellal, who arrives at the scene. He begins to unleash multiple attacks on Acnologia, which do not affect him. Jellal then casts Grand Chariot, but Acnologia eats the Magic, shocking all three Wizards. Wendy wonders what element Acnologia has, who replies that he has none, and that he is the Dragon of Magic. He transforms into his Dragon Form, while Jellal realizes that Magic does not work on him. Wendy decides that she has to fight him because she is a Dragon Slayer. She enters Dragon Force and charges at Acnologia, who begins to charge an attack at her. Out of nowhere, however, the Christina appears and rams into Acnologia. Ichiya opens the door and tells the Wizards to enter the ship. As they board, the Christina begins to lift off, with Acnologia chasing it. Inside, Ichiya tells them that there is a chance that they can beat Acnologia, with blonde-haired woman agreeing with the statement.
The Christina begins to shoot blasts at Acnologia, which do not affect him, while the woman, revealed to be Anna Heartfilia, tells the Wizards that they can stop Acnologia by trapping him in the Space Between Time, a void of nothingness, created when the Eclipse Gate was opened. Ichiya reveals the plan, which is to detour around the void and while Acnologia is chasing them, he touches it and is destroyed. When they reach the Space Between Time, it appears that Acnologia has touched it, but he suddenly rams into the Christina. Anna then realizes that the rift is closing due to Zeref having it under his control.
Acnologia causes the Christina to lower until it hits the water. Erza tells Ichiya to destroy the lacrima that keeps Dragon Slayers from getting motion sick. This causes Acnologia to let go of the Christina, allowing it to speed away from Acnologia. Anna realizes that they must force the Space Between Time back open. As Acnologia continues chasing and damaging the Christina, Jellal decides to distract him, while Anna focuses on reopening the time rift. The tactic fails as Acnologia easily dodges all of Jellal's attacks. Suddenly, Anna notices that the Space Between Time is reopening again, because Zeref is ready to use it for his plan. Jellal decides to push Acnologia into the rift as Erza screams his name in fear. His plan ultimately fails as Acnologia begins to devour Jellal's Magic but little-by-little, he is able to slowly push Acnologia towards the time rift. As the Christina crashes into the ocean, Acnologia grabs Jellal and begins to slowly crush him.
While Acnologia continues to crush Jellal, the Christina suddenly lifts into the air. Anna is revealed to be steering it as she declares that she is going to use the ship to push Acnologia into the Space Between Time. However, the Christina begins to lower because only members of Blue Pegasus can pilot it. Out of nowhere, Ichiya grabs the steering wheel and tells Anna that he cannot let a woman with a wonderful perfume go by herself. Ichiya tells the Dragon to let Jellal go because he must live to protect Erza. Acnologia drops Jellal into the ocean when the Christina hits him, sending him and the ship into the Space Between Time.
Meanwhile, after his battle with Zeref, Natsu meets with Lucy, Gray, and Happy. As they walk towards their guild hall, they notice that Natsu is nowhere to be found. Elsewhere, on a rock in the middle of the ocean, Wendy notices a crack appear in the sky. Acnologia suddenly breaks out of the sky and declares that great power is surging within him. He then spreads his wings and proclaims that the world belongs to him. He then casts Eternal Flare, which sends hundreds of blasts flying into the world and destroying many things. Erza and Jellal notice that Wendy is suddenly in the sky. Acnologia appears above her and absorbs her. Acnologia proudly shouts that all of the Dragons are coming to his time. Around the kingdom, all of the Dragon Slayers begin to disappear.
In the Space Between Time, Natsu lands on the ground and wonders where he is. Acnologia, in his human form, appears before Natsu and tells him that this is his world. Natsu realizes who is standing in front of him as Acnologia shows him all of the Dragon Slayers, who are trapped within crystals. Acnologia says that he has gained space-time Magic from the time rift, and that he will use the Magic to destroy the world. Outside the rift, Anna and Ichiya escape from the rift. They land in the water next to Erza's group. Anna tells them that Acnologia devoured the Space Between Time and gained time Magic. However, this caused him to split in two: a flesh Acnologia and a spirit Acnologia. In the time dimension, crystals begin to appear underneath Natsu's feet, trapping him in place. Suddenly, Wendy escapes from her crystal and frees Natsu. Soon after, all of the other Dragon Slayers escape and join Natsu as they prepare to face Acnologia, who smiles as he tells them he must teach them why people call him the "Dragon King".
The Dragon Slayers and Acnologia continue to stare at each other. Natsu then tells the Dragon Slayers to go as they all leap in the air. Wendy uses Deus Eques to boost all of the Dragon Slayer's physical abilities. While they comment their new strength, Gajeel smiles and says to never underestimate Wendy. He then runs towards Acnologia and uses Iron Dragon's Sword, which easily bounces off of Acnologia. Sting and Rogue run past Gajeel and get ready to attack, but Acnologia blasts them away, causing them to crash into Gajeel. Erik and Laxus run towards Acnologia and begin to use their Magic but Acnologia blasts them away too.
Natsu yells their names as Erik realizes that he cannot hear Acnologia's mind. Acnologia charges an attack at Natsu, while Wendy tells him to dodge it. Natsu is hit by the attack, which creates a huge explosion. However, Natsu is able to block it. The Dragon Slayers begin to comment on Acnologia's immense strength, to which Acnologia asks them if they know why he is called the Dragon King. He tells them it's because when it comes to strength, he is number one. He then tells them that outside the dimension they're in, his flesh form is in the process of destroying the world. He tells them that he will annihilate everything and bring in the end of days. Natsu asks him what is it that he wants, to which Acnologia replies that all he wants is destruction. As the Dragon Slayers look in shock, Acnologia begins to cackle uncontrollably. Natsu tells Acnologia that he will soon find out that it will not just let him destroy it.
Sting and Rogue jump in the air, charging their fists with Magic, but Acnologia sends them flying backwards. Natsu runs pasts Sting and leaps at Acnologia, attempting to hit him with his fire. Acnologia easily avoids Natsu's attacks and punches him in the stomach, sending blood flying out of Natsu's mouth. Erik, Gajeel, and Wendy charge towards Acnologia, ready to attack him, but the Dragon King blocks all of their attacks and knocks them to the ground. Laxus appears behind Acnologia and attacks him with lightning Magic. However, Acnologia slams Laxus into the ground, saying that Magic does not work on him.
Erik then attacks Acnologia, but he blocks Erik's attack and kicks him in the chest. A shocked Erik says that Acnologia caused him internal damage and with only one hit. Natsu yells his name as Erik says that he isn't done yet, and that he cannot just give up and die because he has friends that he must keep safe. Sting and Rogue say that if they lose, they will never be able to face their friends again, and that everyone is waiting for them to come back. Laxus adds that he won't let Acnologia kill anyone, while Gajeel states that they will crush him before he can crush them. All of the Dragon Slayers begin to stand back up again. Wendy tells Acnologia that the legend he has built will end now. Natsu adds that this is Acnologia's final fight. Acnologia merely laughs at this, saying that they haven't even fought yet. He begins laugh at the Dragon Slayers.
Acnologia creates an explosion, and then grins as he asks if that is the best that the Dragon Slayers can do. The Dragon Slayers tell him that it doesn't matter if Magic can hurt him, because they will keep attacking him until it does hurt. They then all agree to take Acnologia down. All of the Dragon Slayers charge at Acnologia, screaming. The Dragon King tells them that their struggling is futile. Natsu jumps at Acnologia, who easily kicks him away. Gajeel tries to hit him, but misses and is kicked to the ground. Wendy also attempts to attack Acnologia, but he blasts her away. Sting and Rogue lung at him, but they are thrown into the ground. Erik does the same but is kicked away as well. Laxus tries to damage Acnologia using lightning, but Acnologia grabs his hands and throws him into nearby crystals. Acnologia turns and smirks as he watches Natsu and Gajeel using Fire Dragon's Roar and Iron Dragon's Roar.
As Acnologia cuts through the attack, Sting uses Holy Ray, however, Acnologia avoids all of the blasts. Rogue and Erik use Shadow Dragon's Roar and Poison Dragon's Roar, but both are caught by Acnologia as he lands on a crystalized structure. Wendy then uses Sky Dragon's Wave Wind, which destroys many crystalized structures. Laxus jumps into the air and uses Lightning Dragon's Heavenward Halberd. However, Acnologia is unfazed by all of the attacks and uses a roar that destroys almost everything around him and knocks all of the Dragon Slayers to the ground, all of them terribly injured and defeated, save Natsu.
Acnologia smirks as he tells them that this is where it ends for all of the Dragon Slayers, because he will not allow a single Dragon to be left alive, as that is what it means to be a Dragon Slayer. Natsu simply laughs at this and tells him that even if he kills them, he is still a Dragon, and that there will always be one Dragon left. Natsu also adds that they are not Dragons, but humans with the power of Dragons. He goes on to say that true Dragons are strong, noble, and nice. This angers Acnologia greatly who tells him that he lost everything to Dragons when they ate his family, burned his town, and slaughtered everyone around him. He then asks Natsu how Dragons could possibly be nice. Acnologia creates a huge explosion around him, which engulfs Natsu. However, Natsu is unharmed, and he tells Acnologia that there are all kinds of Dragons, some nice and some evil, and also some who are going to defeat Acnologia. Suddenly, Wendy gets up and tells everyone that she is gathering up all of the Dragon Slayer's power and giving it to Natsu. All of the Dragon Slayers then shoot all of their Magic into Natsu, creating a rainbow flame. Natsu declares that he is gathering all of their power and turning it into flame. He then adds that this is the power of the Seven Fire Dragons.
As the Fairy Tail Mages use their Magic to trap Acnologia's flesh form in Fairy Sphere, Natsu declares that he has got what Lucy and the others had sent to him. Natsu shouts as he is surrounded by the rainbow flame, while Acnologia tells the Dragon Slayers to behold his power of destruction, as he charges his fist with Magic. Acnologia tells Natsu that even if everyone combines their powers, they cannot defeat him, as outside the Space Between Time, his flesh form begins to break out of Fairy Sphere. Acnologia suddenly starts to go insane as he shouts that he must destroy everything, and that he must bathe in more Dragon blood. The Dragon Slayers comment on Acnologia's new personality, while Natsu looks at Acnologia and sadly states that Acnologia can no longer end this on his own anymore. As Acnologia moves to attack, he realizes that he cannot, because in Magnolia, the entire continent of Ishgar is using their power to keep Acnologia trapped in Fairy Sphere, preventing Acnologia from moving. Natsu charges at Acnologia as the others cheer him on. Natsu creates a giant fist from the Magic and runs towards Acnologia.
Acnologia turns towards Natsu and sneers at him. He then tries to block the attack, but realizes that he can't because he is unable to move the arm that Igneel ripped off a year ago. A shocked Acnologia can only watch as he is hit full-on by the giant fist of Magic. This sends Acnologia flying through many crystalized structures and causes him to roll on the ground. As he slowly flies through the air, he says to himself that it isn't enough and that he doesn't have enough blood, destruction, and tears, as the Dragon Slayers look on. Acnologia states that he must destroy everything and everything must be his. Natsu tells him that there is no way everything can be his. He tells Acnologia that's why he must take good care of everything that he gets and to not be greedy. Natsu says that as long as he has got his friends, he does not need anything else. Acnologia looks at Natsu as he begins to disappear. He tells Natsu that he is truly worthy of being the king before disappearing completely. Natsu simply states that he doesn't want to be king.
Meanwhile, in Magnolia, Acnologia's flesh form disappears as well, shocking all of the Wizards. Lucy and Happy both realize that Natsu and the other Dragon Slayers have won. Everyone begins to cheer and hug, happy at their victory and that the war is finally over. Suddenly, the sky cracks and all of the Dragon Slayers fall out of it, screaming. Natsu falls directly on Lucy and Happy, who welcome him back. The other Dragon Slayers reunite with their friends as everyone continues to cheer. Lucy says that on that day, one era of the world came to an end. However, because one era ended, another one began.