My brother and I came up with an idea for hacking FF6 that isn't like anything I've ever read about on here.
It started with a conversation about Sabin. His character arc is more or less wound up by the time he joins your party. His driving motivation after that becomes "let's beat up the Empire raaah," and he isn't required to be in the party after the Battle of Narshe for the rest of the game. As the game stands, Sabin is used mostly for the characterization of the other characters both directly (as a contrast to Edgar's stoicism) and indirectly (because the other characters mostly have really heavy emotional arcs).
My brother then said, "What could we do to change that?" and we got to talking. I'm now reporting what we came up with.
My first idea was to give Sabin a girlfriend who, after he sees her again in S.Figaro in the WoR, would then report that she had a 'bun in the oven,' but my brother rightly mentioned that if we made her as happy-go-lucky as him, it would be pointless filler, and if we made her a heavier character than him, it would make his character too emotionally heavy, so we dropped this idea.
I happened to mention that Vargas is completely dropped from the story with no further explanation, despite him being the main thing which leads to you recruiting Sabin, and I began to dream up a scenario as my brother kept asking leading questions.
So, what we eventually came up with was a story in which Vargas ends up being the "Sith Apprentice" to Kefka's "Sith Lord," as it were. After he's beaten by Sabin (this all happens offscreen and is just alluded to later), Kefka (who would have been in the area after all) offers to give him a fast-and-unauthorized Magitek Infusion to augment his martial arts abilities, and get back at Sabin.
The next time we see Vargas, he is calling himself Dadaluma, and whether Sabin is in the party at Zozo (and fights him) or hears about it (when the rest of the party convenes after the cutscene with Ramuh), he decides that he is dead-set on going to the Empire with Locke and Celes. This does reduce the available party slots to 1 for optional characters, but we thought "Why put all this work into a B plot through the game if Sabin isn't ever required?"
When you get to Albrook, there is an NPC whose dialogue would be changed to allude to some sort of trouble with a new Imperial Officer in Tzen. Vector would have to be made into a sort of 'broken bridge' for this to play out, and you would have to go to Tzen and find Vargas there barking orders at the townspeople. This would be where the exposition about him having joined forces with the Empire to defeat Sabin would happen, and you'd fight him and some cronies before he'd hightail it back to Vector.
Once that event was complete, you'd be directed to visit Maranda, whereupon someone with an axe to grind against Vargas personally would give you the means to enter Vector. This aspect of the B Plot for Sabin is something we'd need to work on harder; I'll admit that it was rather unsubstantiated in our discussion.
Once you got into Vector, everything would play out as it does in Vanilla FF6, but after you'd gotten about halfway through the Magitek Facility, you'd run into Vargas, who'd once again battle the party, revealing that he's had a Magitek Infusion, and this is what is increasing his power over time. After beating him, you'd end up seeing the scene with Kefka, Shiva and Ifrit, and continuing the Mtek Facility as normal.
Then, instead of Number 024 (who sucks and is pointless to the story), we had the idea of Sabin and Vargas having a duel to the death, where Sabin directs the other party members to 'stay out of it.' Vargas is killed here, and the rest of the WoB plays out as normal.
Now, in the WoR, IF you have recruited Sabin, and go into Figaro Cave (regardless of whether you already have the Falcon or not), and visit a certain location (which we also did not substantiate very well), we had the idea of Sabin hearing Vargas' voice and being freaked out (sort of a callback to FF4's Mist Cave). At that point, a flag would be set...
This flag (I'm guessing it would have to be some kind of ASM Instruction) would state that if Sabin was in the party, and Shadow was not in the party, and you stayed at an Inn, Sabin would have a nightmare about Vargas (which also has yet to be fully written).
Finally, when you get into Kefka's Tower, take Party 1 across the switch, and turn left or right, then have either Party 2 or Party 3 go the other way, and finally have either Party 2 or Party 3 complete the whole deal by going down the center, the game would run an ASM Instruction which checked if the party which is standing on the center switch contained Sabin. If so, Guardian (in the next room) would be replaced with a Demon-Possessed Vargas who offers to wage one last battle against Sabin, which of course he would lose.
At that point, Vargas, stripped of all his self-determination by this demon possession, would reflect on how his desire for power ended up taking away his freedom, in the end, and muse to Sabin that giving in to rage is ultimately an abuse of free will.
This has the effect of giving Sabin a relevant character arc, while using assets which are already in the game (MOSTLY), and not making him too much of an emotionally heavy character. It also makes use of things which are already in the story, and in a way vaguely calls back to Count Borgen in FF2 (Famicom), though this is merely a coincidence.
It would require sacrificing lots of the unused text boxes in the main dialog script, as well as the "Real Siegfried" and "Kaiser Dragon" battle captions, and it would also require coding a couple of events in the game from scratch, which I have no idea how to do.
But that's the skeletal structure of what we came up with.