Final Fantasy 7 Remake Intergrade Ending Explained: What EVERYONE Is Missing
1. "The Planet's Fate"
Though Zack is dead, Aerith mentions her "stomach being in knots" in an exchange with Cloud - likely because Zack has arrived at his final resting place, post-Harbinger's defeat.
Zack's presence at the church makes Aerith feel something in regards to knowing she has to break Cloud's heart, as in Chapter 14, she actively tells Cloud not to fall in love with her. This could be because she always ends up with Zack, as seen in 2005's movie.
We can assume based on Zack's location in both Intergrade and Advent Children, that he spends his time waiting at the doors of the church, to eventually leave together with Aerith.
Now, does some energy in the cosmos mean that Zack returns to defeat Sephiroth, with he and Cloud busting out twin omnislashes for the final fight??
Almost DEFINITELY. If Zack is divorced from time and space, living in some ethereal spot until he can finally be free, there's nothing stopping FFVIIR's writers from having him manifest in the final dual, as Sephiroth is cleary able to teleport and conjure himself in a variety of spots too.
Ultimately though, Zack died when Shinra ambushed him and Cloud. Cloud took the Buster Sword and everything played out as it's supposed to, because that is the PLANET's fate.
Final Fantasy VII, for as big and blustery as it's gotten, is still about protecting the planet, which is the core theme and message of the entire mythology.