The big twist in Final Fantasy VII Remake is that the characters are able to defy their fate and deviate from the story of Final Fantasy VII. The characters are no longer bound to the events of anything that happened after the Midgar section of Final Fantasy VII, which includes Advent Children and Dirge of Cerberus.
The question that fans have been asking themselves is what caused the deviation of the timeline in the first place, other than the developers needing an excuse to let fans know that the story will be different going forward? It seems that Sephiroth is the key to these changes, as his actions and words suggest that he knows more than he is letting on. The question now is how Sephiroth gained this new knowledge and why the Whispers are intervening? It's possible that the Sephiroth we see in Final Fantasy VII Remake is the same as the one from the original timeline and he has traveled back in time to change the course of history.
How Sephiroth Survived The Events Of Advent Children
In Advent Children, Sephiroth is reborn through a combination of Jenova cells and a person called Kadaj. Sephiroth was unable to become one with the Lifestream, as his body contain alien materials from Jenova's body, so he can resist joining the planet through force of will. He discovered a way to create a new physical body, which involved creating lifeforms within the North Crater and sending them out into the world to track down Jenova cells, which could be repurposed into a new form. Kadaj is one of these lifeforms and Sephiroth's plan works, but his new body is destroyed by Cloud at the end of the movie.
Sephiroth's plan might have been foiled, but he can still return in the future. The spin-off novel called On the Way to a Smile confirmed that Sephiroth cannot be absorbed into the Lifestream, so long as Cloud is still alive. Sephiroth is obsessed with getting revenge on Cloud, so he has every reason to linger on and continue to seek a way to return to the land of the living. Cloud is still active as of the events of Dirge of Cerberus, so it's possible that Sephiroth could take on a new form after Advent Children.
The Untold Story Of Genesis & Weiss
The story of Final Fantasy VII ends with a flash-forward to 500 years in the future, as Red XIII brings his cubs to the ruins of Midgar. It's clear that some other major event happened before then, based on the secret ending of Dirge of Cerberus.
If the player collects all of the hidden G-Reports in Dirge of Cerberus, then they will see a secret ending to the game. In this new ending, Genesis from Crisis Core finds the body of Weiss the Immaculate, says that they have much work to do, and he sprouts a wing. Genesis flies off with Weiss and we have no idea what happened next. According to the Final Fantasy Wiki, the Crisis Core Complete Guide explained that Genesis returned to protect the planet, but it doesn't explain from what? At this point in the story, Jenova, Sephiroth, the Tsviets, the Weapons, and the Shinra Corporation had all been defeated. What was Genesis returning to protect the planet from?
Sephiroth Pulled A Quantum Leap
It's possible that Sephiroth was able to return in the future and he gained the ability to manipulate time. Crisis Core established that there is a goddess figure within the Lifestream, called Minerva, who can perform incredible feats. Minerva's power is such that she was able to bring Genesis back from the dead for some unknown purpose.
If Sephiroth can maintain his existence within the Lifestream, then it's possible that he could become a threat to Minerva at some point. This might be why she brought Genesis back to life and why Genesis needed Weiss' aid. Genesis returned to protect the planet from Sephiroth, but he failed in his mission, and Sephiroth was able to go back in time to try and influence events going forward. Sephiroth claims that he is protecting the planet, but he still wantonly murders people. It's possible that Sephiroth is still seeking godhood and he wants to use his knowledge of events to complete his plan without being foiled. It's unclear why he wanted Cloud's help to defy destiny or why he brought him to the "edge of creation" itself, which is a secret that is likely being saved for future entries in the remake series. Sephiroth's motives are one of the biggest unresolved mysteries in Final Fantasy VII Remake and it's possible that his knowledge will involve tying up some loose ends from the previous Final Fantasy VII spin-offs.
Final Fantasy VII Remake is available now for PlayStation 4.
Source - Final Fantasy Wiki