Merge and reboot the worlds into one (as if dimensional boundaries and time travel might not exist.) Redraw and adapt character relationships, landscapes, power structures, power levels, and motives as necessary.
Whether you have megacorporation vs. empire vs. resistance vs. chaos.
AVALANCE, Returners and NORA plus others might form a resistance group against the megacorp and the empire. They might operate between poorly monitored corporation/imperial cities and neutral trade cities. Operations funded by noblemen like Banon or a mysterious benefactor a.k.a. Rufus.
Empire might consist of several nations with emphasis on militaristic conquest, with Archadia, Baron, Figaro, and Dalmasca... employing the use of ancient resources as weapons (aethryte), superior chocobo forces, airships and cannons powered by crystals, coercing summoners to fight for them.
Megacorporation might consist of with several corporation leaders such as Rufus, Dysley, and Gestahl ~ utilizing magitek weaponry, enslaving espers in magicite, airships powered by magicite, kidnapping summoners to create magicite out of eidolon powers, etc.
And chaos might be a group of ancients, insane bastards, or warmongers planning to do the eradicate the world. Manipulating the strings of others to make this come to fruition. Be that a crazed engineer, a Kefka, a hidden agenda Dysley, a Yuna-plz-marry-me Seymour, making Sephiroth go nuts... again, liches, dark knights, rallying beastmen, or eidolons convinced that man-and-mooglekind is just unsalvageable (because they do wicked crap like enslaving espers in magicite and use aethryte (life stream?) as a weapon).
Maybe some engineering organization that tries to remain neutral, let's call 'em C.I.D. (crazy indigenous dastards that they are) that have split their allegiances.
Perhaps story lines are more event driven, with multiple characters that can be selected per mission.
i.e. a train mission led by the liberation... with Snow and Tifa as brawler types, Lightning and Cloud as sword types, each with their own play mechanic. Snow might have a taunt ability. Cloud's mechanic may be interchanging his swords. They hijack a train maybe as an attack on the megacorporation akin to the FF7 opening mission, end up fighting against Turks, a Judge and Archadian troops leading their own assault, and a mentally warped Terra piloting a new magitek warmech for a boss (free the esper girl). Maybe on Hard mode she would transform into esper mode while piloting.
Or a concert / opera house mission set as a trap to lure Setzer (unpredictable sexy coin-flipping bastad in an airship causing trouble for megacorporation and empire alike OR the resistance want to utilize him for their cause). Celes might represent the megacorporations as an opera singer (mayhaps using a magicite of a Siren), Yuna goes along on behalf of the resistance, and throw in some third character to represent the Empire (does Garnet sing?). Throw in a Bayohne (or if he's taken, Ultros) + a Judge to monitor the ground situation, Resistance sneaking around up top, and some Megacorp elites who have a second motive of kidnapping summoners. If the players choose a songstress, they control the lines that are sung to pull a convincing performance that may buy additional time to capture Setzer. If not a songstress, the player will be responsible for preparing the assault against Setzer, sabotaging other factions and avoid interrupting the performance to corner the gambling man.
And yes... these might have been plots ripped from older table-top gaming sessions under a Final Fantasy ruleset... minus the celebrity characters. Eheheh.