By chronological order (I know it won't be totally accurate):
1. Instead of a simple face-off, Lucy and Cana will fight Brandish. The latter will low-diff them during this fight, which will be interrupted by Ajeel's sandstorm. After Ajeel's defeat, Cana will knock out a sneezing Brandish, as in canon.
2. Ajeel will face Juvia, Wendy and Carla, instead of Erza. As Fairy Tail wizards know his magic, they will team up people with most advantages again him. Girls will give Ajeel a good fight (Juvia will use Water Make Magic) but then he will use his sandstorm and give a lot of trouble to them. Bisca will snipe him due to her instinct. Wendy and Juvia will then deafeat Ajeel with an Unison Raid, combining Sky Dragon's Roar + Water Cyclone.
3. As in canon, Natsu and Gajeel will fight Ajeel's troops, **but this time without Wendy but with Erza's and Gray's help.
4. Mira, Elfman and Lisanna will defeat, as in canon, Wall's soldiers, by switching up opponents but this time without Gray and Juvia.
5. Fake! Wall's fight remains the same.
6. Natsu and Zeref's fight remains the same.
7. Brandish-Lucy-Aquarius scene occurs like in canon.
8. God Serena didn't low-diffs Gods of Ishgar. Instead, they give a lot more trouble and he is forced to use a Dragon Slayer Secret Art to defeat them. Acnologia didn't show himself, then God Serena isn't killed.
9. Erza, Gray, Wendy, Juvia and Laxus go at Hargeon like in canon while Gajeel, Levy, Lily, Mirajane, Elfman and Lisanna went to North.
10. Hargeon's side: Wendy and Chelia fight Dimaria, Ultear comes in, Dimaria actives her God Soul: Chronos, Ultear uses Third Origin on Chelia, **the latter extreme-diffs Chronos-Dimaria. She losts permanently her magic.
11. Laxus confronts Wall Icht and defeats him like in canon with Red Lightning Dragon Mode.
12. Natsu and Lucy fight Jacob, after Lucy released all Fairy Tail members with Gemini Star Dress, they defeat him with an Unison Raid: Fire Dragon's Shining Impact.
13. Erza, Jellal and Kagura's fight against Ninehart occurs almost like in canon, the only change will be that Jellal uses Abyss Break to almost kill Ninehart after seeing Erza grievously injured.
14. Wendy vs Historia! Ezel, Laxus vs Historia! Hades, Juvia and Meredy vs Historia! Keyes and Historia! Zancrow occurs like in canon while **Historia!Ur vs Gray and Lyon fight will end by Historia!Ur telling to Gray and Lyon how she is proud of them.
15. As in canon, Natsu, Lucy, Brandish and Mest leaves guild to negotiate with August, Mest alter Brandish's memories in order to kill August, the latter enter in his "red rage mode" (this how I call this form)
16. Gajeel vs Bloodman will occur like in canon.
17. Irene and Acnologia will fight a little** before the Scarlet Despair uses Universe One.
18. Juliet and Heine won't give trouble to Mira, she will one-shot them with Alegria Form from the beginning. Then Irene appears, she attacks Mira, the latter gives her a decent fight before getting one-shot by August.
19. After August & Brandish pick up Irene and Larcade pick up Dimaria, the Spriggan 12 reunites as in canon
20. Natsu, Lucy, Gray, Erza, Juvia and Happy are reunited with each other and attacks Alvarez Army. They are joined by other Fairy Tail wizards and other guilds.
21. Mirajane attacks Jacob and beats him easily by using Satan Soul: Kyoka, she amplify all his senses to make him suffer at hell, then he is unable to fight.
22. Elfman's and Lisanna's fight against Ajeel remains the same.
23. Rogue and Minerva fight Historia! Bloodman and Historia! Wall, however, **Rogue will enter in Dragon Force and Minerva in Neo-Minerva form.
24. God Serena then appears and attacks the wizards. All his elements are shown and used: Gale Dragon (Wind), Sea King Dragon (Water), Cavern Dragon (Earth), Purgatory Dragon (Fire), Voltage Dragon (Lightning), Arctic Dragon (Ice), Holy Dragon (Light) and Darkness (Shadow) Dragon Slayer Magic. Natsu, Lucy, Gray, Erza, Wendy, Juvia and Loke fights him and casts an Unison Raid to finish him. God Serena is slightly injured and casts a new Secret Art. Gildarts shown himself and destroys Serena's spell. Their fight is much longer because Serena isn't an Historia but Gildarts ends the fight by high-diffing Serena.
25. Natsu, Lucy, Gray and Juvia are confronted to Invel. As in canon, Brandish takes Natsu, Lucy and Happy with her. Gray begins to fights Invel with Juvia's help. Then Lyon comes in and helps Gruvia. Gray enters in Devil Slayer Mode and tries to eat Invel's ice but Invel is revealed to be a Ice God Slayer. He no-diff Gray, Juvia and Lyon and use Ice-Lock on Gruvia while Lyon is unconscious. JUvia decides to sacrifices herself, she saves Gray with Water Make: Blood, Gray enters on Rage Mode because of Juvia's "death" and absolutely destroys Invel.
26. As in canon, Ninehart, enchanted by Irene, will attack Natsu's group and Brandish, he will get one-shot by Natsu. Brandish will amplify Natsu's tumor's size, then he pass out. Lucy will begins to fight her as in canon, but their fight will become longer, Brandish won't hold back and Lucy will summon more spirits, use more Star Dresses, and even cast Urano Metria. After used her strongest spell, Lucy will run out of magic power and almost pass out while Brandish will decide to stop to fight, although she could beat Lucy. Dimaria then comes in, stabs Brandish and kidnaps Natsu and Lucy.
27. Dimaria tries to kills Lucy as in canon, the latter passes out and wakes up a few moments later, to see Dimaria who get destroyed by Natsu, who become END. Porlyussica, Brandish and Evergreen then arrives.
28. Natsu (in a full END form) encounters Gray (under demon's control). Their fight is much longer and violent than canon.
29. During this time, Makarov will use Fairy Law and will stay dead after its use.
30. Jellal and Crime Sorcière will get destroyed by August as in canon.
31. Lucy and Juvia (who was saved by Wendy) will interrupt Natsu and Gray's fight, instead of Erza.
32. Natsu, Gray and Juvia all pass out, as in canon. Then Irene appears and attacks them. Lucy, Happy and Carla leave with Natsu, Gray and Juvia unconscious while Erza and Wendy will stay here to fight with Irene.
33. Larcade battle occurs like in canon.
34. Irene fights Erza and Wendy. It occurs like in canon until Wendy recover her body. She enchant Erza, Jellal, who escapes from August, then comes in the fight and helps her (Erza) to fight the Scarlet Despair. Irene goes in her dragon form and breaks all Erza's bones. Jellal become angry and tries to attack Irene, who no-diff him. She casts Deus Sema. Jellal destroys the meteor by using his own Sema xD. Wendy then enchant Erza and Jellal to give them Dragon Slayer abilities. They hurt Irene who come back to her human form. Jerza try to fight Irene but they are too weakened to do anything. Irene is ready to kill them but Erza smiles and she (Irene) remember her when she was baby. Then she stabs herself but Wendy, by how kind she is, decides to save her and pass out after using all her magical power. Irene heals Jerza and Wendy with her enchantments and leaves.
35. August battle happens like in canon.
36. Natsu dreams about other Dragon Slayers and Zeref and learns more about his past. But none dream about Igneel and Dragon/Demon Seed.
37. Universe One is then cancelled by Irene.
38. Jellal spawns directly at guildhall (while Erza and Wendy appears somewhere at Magnolia) and confronts Zeref. He gives him a decent but short fight before getting interrupt by Gray's arrival.The latter tries to use Lost Iced Shell as in canon but is stopped by Natsu, who's with Lucy and Happy. Gray, Jellal, Lucy and Happy leaves, letting Natsu with Zeref.
39. The Fire Dragon Slayer begins to fights Zeref. When Larcade arrives, he is very angry to see Natsu and attacks him. Zeref is really happy to see his two most powerful Etherious fighting each other but finish by brutally one-shot Larcade and kill him. Natsu gets angry because Zeref killed his own comrade. Their fight continues until Zeref gets Fairy Heart. Then Natsu is stomped as in canon and is almost killed.
40. On Lucy's side, Jellal leaves to return with Erza. She rewrite END's book, which allow Natsu to stand up. Then he falls under END's control and overpowers Zeref, who gets destroyed by his most powerful Etherious. Lucy is almost dying but is saved by Gray's Devil Slayer Magic. Then she runs towards the guildhall to find Natsu, who's always under END's control. He brutally attacks her while she tries to bring him back to his senses. Gray tries to protect Lucy, but he can do nothing. Then Lucy hugs Natsu, whispering to him some words (ask me what in the comments and I will let you know).
41. Christina-Acnologia chase scene happens the same way as canon, except the beginning. As Irene isn't dead, Acnologia won't stomp her corpse but he will attack Erza, Wendy and Jellal anyway.
42. Dragon Slayers are absorbed by Acnologia's spirit in Time Rift and begin to fight him. They all enter in Dragon Force (even Gajeel, Cobra and God Serena) and significantly damage him with Unison Raids.
43. At Harujion, Ishgar mages are fighting with Acno's body until Irene appears. She enchant them with Dragon Slayer abilities, so they would be able to damage Acnologia's body.Lucy then have the idea of Fairy Sphere and actives it. Thanks to Meredy, all Ishgar's wizards give Lucy their magic, which is enough to weaken Acnologia.
44. Irene use a very strong spell to bring back Dragon Slayers and Acnologia, who is really angry about this and begin to destroy everything around him.
45. Irene, helped by Wendy, use one of her most powerful enchantments, Deus Draco to turn Natsu into a dragon, which exhausts her at hell. Dragon Natsu fights a weakened Acnologia and kills him by the same way he killed Igneel.
46. About epilogue, I won't change it except I will make Erza/Laxus Ninth Guild Master, Crime Sorcière will be disbanded and I will confirm main ships as NaLu, Gruvia, Jerza and GaLe but also side ships like Miraxus and StingYu.
Thoughts about this rewrite? (it comes from my Reddit account)