TL;DR: Sephiroth and Cloud switch roles.

Forgive me my crumpled narration, I am as far away from a writer as I can possibly be, feel free to skip.

Based on a plot that I thought about two years ago. To be honest, I don't like it quite as much as I did at first, but whatever, I wanted it to exist in some way.

Plot starts with AC!Cloud time-travelling to the time right before Nebelheim incident, when Sephiroth can already hear Jenova, but isn't completely broken mentally yet.
Cloud kills Jenova - well, he thinks he does, but actually becomes a host for her.
He believes that everything he does after that is for the sake of saving the Planet, but actually he helps Jenova.
He sees Jenova as adult Aerith (she took this image from Cloud's mind), because she is the one he would trust the most, especially considering that Aerith have already spoken to him from Lifestream in his original timeline.

Jenova still wants to get Sephiroth, but it becomes more difficult for her, because she can't talk to him as his mother since it would definitely be very suspicious to Cloud. For the same reason she can't tell him that he is a Cetra and deserves to rule.

She can only cherry-pick some of Cloud's memories and show it to him. Like, "this will happen if you don't help us". It doesn't work well and Sephiroth resists. Also Cloud avoids getting close to him as much as he can. There is not a lot of opportunities for contact since Sephiroth is still in Shinra.

First Cloud (by Jenova's persistance) destroys one of the reactors. He drinks mako, because Jenova needs more power. She tells him that the Planet itself wants to share its power with him.

Cloud grows wings. White, three on each side. It's very painful for him, but Jenova says that it's Planet's gift, so he should be grateful.

Jenova still has no direct control over him, so she has to explain everything she wants him to do, otherwise he won't go through with it.

Under mako's influence Cloud's will starts to decrease. Jenova convinces him that he should kill Weapons and take their power, because he himself must become a Weapon.

Cloud stops eating, only drinks Mako.

After the first Weapon's death other ones come to life. Two of them are killed by Turks and Soldiers, the rest - by Cloud.
His Will continues to decrease. He needs more and more mako.

At the same time Sephiroth meets seventeen year old Aerith - the real one. Even before he was suspicious, now it becomes even stronger.
Also the voice in Cloud's head really reminds him about the one that wispered him about mother's love.

By that time Cloud has absorbed almost all of the Weapons, only Chaos and Omega remain.

Wings require a lot of energy. Cloud loses weight.

Jenova needs to get rid of Chaos somehow, so she says that people of Nibleheim might still be under Jenova's influence, so Nibelheim should burn.
Cloud burns Nibelheim down. Cloud's mother sees him and tries to stop him, but it doesn't help. He is half-crazy by that time.

Cloud carries Tifa out in his arms. Jenova says that every resident of Nibelheim has Jenova's piece inside of them, but Cloud refuses to kill Tifa and he becomes suspicious, so Jenova yields. Cloud keeps Tifa with him to watch her in case Jenova awakens.
Tifa sees his eyes, they look like Jenova's. She runs away.

At the same time Zack, Aerith and Sephiroth go for Cloud's head. They meet Tifa on rthe road and she decides to go with them.

Cloud sees them and thinks that everyone betrayed him. He loses the rest of his control and transforms into a monster. In this form he can't really fly, but he makes powerfull leaps into the air. Aerith's flowers suck the life out of his body. His eyes are closed.

They fight him. At some point during the battle he feels Aerith's presense. She is scared. It breaks him and gives him some of the control. He opens his eyes and flowers start to get out of his body together with blood. He screams.

Aerith summons Holy and Cloud is thrown into Lifestream.

Couple of month later his monster form is found in North Crater frozen inside a huge piece of ice.
Planet really made him its Weapon.

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