Lisanna is dead and Natsu blames himself for not going along with her on the S-class mission. Drowned in sorrow he runs into an old man, literally, and makes him drop a book. Picking up the book to give it back to the man only to find he is gone. Natsu wondering what the book is reads the title to which it says 'Alchemy Magic: The Transmutation Circle'. Finding it interest he starts to read it and finds out it is a Lost Magic that can do different things. He keeps reading and finds out that it might have the power to bring Lisanna back to life. Hoping it is true makes a promise to learn everything about Alchemy Magic to bring Lisanna back to life. This is a Natsu and Lisanna relationship with Levy acting like a sister to Natsu.
Natsu spends 6 months learning Alchemy magic and how to perform the Transmutation Circle.
Natsu performs the Transmutation Circle and learns everything about Alchemy Magic, but loses left arm and blames himself for seeing Lisanna (The Black Creature) dying twice.
Natsu gets a new left arm that is made of the hardest material so it wouldn't break and leaves Fairy Tail for 1 and half years to learn more about Alchemy Magic and train to become stronger. Happy isn't with him for he wants to do this alone.
Gray meets Lucy not Natsu.
Natsu learns Flame Alchemy Magic (Which he can eat if he wants), knows how to make different weapons from swords, spears, and different guns, he is smarter and more mature, but not mature enough not to get into fights he just cause them now. Stronger to be S-class now. Learns about the philosopher stone, but does not know how to make one.
Meets up with Erza, Gray, Lucy, and Happy to take care of lullaby and goes back to Fairy Tail. Fights Erza.
Mystigan comes and Natsu doesn't fall asleep. Gets into a fight with Laxus and laxus tries to shock him but grabs the metal arm that is covered by a coat he wears with a glove and everyone sees it.
Natsu finds the S-Class mission from the cannon because there is an extra item that says to be a book and a Red stone.
Completes the S-Class mission and saves Ur by using the Philosopher stone he gains from the mission. Ur needs to rest so she will not wake up until the middle Laxus incident to try to become Fairy Tail Master
They come back and Natsu throw himself into studying the book. Levy sees the book and asks what it is and Natsu explains what he is doing. Levy decides to help him anyway she can.
Natsu doesn't go on the theater mission and stays at the guide, however the research that he and Levy did was destroyed when the guide was attacked.
Natsu trys to repair the Guide with Alchemy but the wood is to old to repair it completely. Levy is interested in Alchemy so Natsu starts to teach her.
Fairy Tail vs Phantom Lord is just like the cannon with Natsu using Alchemy Magic and fighting Jose a little before Master shows up.
The rest is cannon with Natsu using Alchemy Magic and being stronger.
When it gets to the day before the festive Natsu and Levy find out that a making a stone takes human lives. Natsu refuses to make one and decides a way to find another way to bring Lisanna back to life.
Natsu fights Laxus and Laxus says that he is weak because he even lost his arm. Natsu then explains how his left arm from trying to bring Lisanna back to life, try to find and make philosopher stone, not going to make one and why he is trying so hard to bring Lisanna back to life. Because he loves her. Everyone is shocked to find out what has done. Natsu and Laxus fight with Natsu barely winning on his own.
When everyone comes back from edo and Lisanna is found out to be alive Natsu breaks down crying, but runs to her grave and starts digging up the body that brought back to find out that it was Lisanna at all. He is even more happy and feels a lot of weight lifted off his shoulder.
Mira tells Lisanna what Natsu has done and Lisanna thanks Natsu by rewarding him with a kiss, which then they start dating.
PM if you want to do this story. I will help in anyway I can.