Here's a really horrible idea:

Shinra builds a time machine and warps ahead of time, to the world where Mako Reactors drain energy from Spira. He finds a guy called Sephiroth, who warps to Yuna's time period. Sin also returns for no reason, and Sephiroth implants Sin full of Jenova cells and takes control of it. Tidus, Yuna and others start a new journey to find the missing warrior Cloud who was rumored to be the only one who can defeat Sephiroth. There's a side story that involves Auron and a girl called Aeris working in the Farplane to help our heroes with their adventure.