Thanks to TotK, we know that Ganondorf's seal broke because of the Great Calamity of 100 years ago, not BotW's present day story. Which means the Great Calamity of AoC should still weaken his seal like on the main branch of the timeline, however this time we're on a new branch and 106 years later there won't be a hero and princess combo to save the day anymore when Ganondorf wakes up. So you would think that doesn't fit with TotK, right? UNLESS...
... Unless we consider events that are unique to AoC's timeline, as well. First we should establish what we know about AoC's timeline split. We know that Terrako had to have gone back in time pretty far comparatively, because Link didn't yet have the Master Sword and hadn't yet met Zelda and Daruk the ways BotW described they did. The very start of AoC must happen much earlier on than the earliest point we ever see in BotW's memories. Knowing that, it makes sense why things happen so much differently than the history BotW's memories painted. We can assume there were so many more monsters that massive-scale battles the likes of which were unheard of in BotW's history became necessary because Astor and Harbinger Ganon were going around creating more monsters for the purpose of expediting the Calamity's revival. We never hear of Astor in BotW's history, because Harbinger Ganon wasn't around to choose him. So because of these two mucking things around, the Calamity's revival actually happened earlier than it did in BotW's history. This is important information for later.
So we know that because this is a timeline split that occurs just before the events of BotW's 100-year history, the setups of TotK's history still apply. On the main timeline, it took 106 years for Ganondorf to wake up after the Great Calamity weakened his seal. On the split timeline, the Calamity was averted, but the damage was still done, and the battle dragged on longer and had Astor and Harbinger doing things that never happened in BotW's history. Most notable of these is fully reviving this timeline split's Calamity Ganon, which we know was done by Harbinger Ganon absorbing Astor and assumedly merging with the Calamity Ganon that was already present in this timeline. We know they had to become one at some point because when they defeat him, Calamity Ganon is gone and the Calamity is over. So he did in fact fully revive, something he didn't get the chance to do in BotW's history because Zelda stepped up to seal him away for 100 years while he was still a cloud of malice. Because of this major difference, and because of the connection between Calamity Ganon and Ganondorf, I think it's fair to propose that this split timeline's Ganondorf can wake up after a similar timeskip as seen between BotW and TotK. Meaning, we can still do a "6 years later" after AoC's ending for this and it would still make sense. TotK's prologue can still commence as it did on the main timeline.
So how could this work here? We can't send AoC's Zelda back in time because even in this timeline the Light Dragon should still exist. As a matter of fact, on this timeline we'd end up with two Zeldas and two Master Swords. Kinda awkward, huh? Here's how I think we can make that a little less awkward...
Gloom starts seeping out as it did in TotK. Link and Zelda go under the castle to investigate as they did in TotK, BUT this time they have Terrako with them. That will be the key that changes how this goes. Link still gets his Master Sword and his arm messed up, but Terrako is the one to intervene and prevent Zelda from getting yeeted back to the past by her sacred stone. Call it plot magic or triforce magic or whatever you want. Instead he yeets her up to the Great Sky Island while Rauru does the same to Link as in TotK. Upheaval still happens. However this time we can't really have several weeks or months pass from this point to when Link wakes up, yeah? So instead of starting the Great Sky Island chapter as Link, you would start it as Zelda and Terrako as Rauru guides them across the island to find Link, to parallel TotK. Fighting through a Warriors map full of Soldier Constructs with Link as the end goal. He would hold on to the Decayed Master Sword and the Master Sword weapon itself would become unavailable to use in-game for a while. Zelda would gain the Purah Pad as a 4th tier of her Sheikah Slate weapon. This is where we can diverge to make a Warriors-themed story, and this would be the start of Chapter 8 in AoC.
Now, for here, we can mirror the story progress from the early chapters of AoC. The Great Sky Island can be CH8M1, and then we can go to CH8M2 on the surface and use an adjusted map of North Hyrule Field and Castle Town that we see in "All Hyrule, United"; adjusted to account for the changes in TotK like fallen blocks and Lookout Landing, which was created to research the gloom and then repurposed into a base to search for Link and Zelda after they went missing. Link and Zelda evacuate the town and reunite with King Rhoam who is still alive on this split. Also, have King Rauru's ghost accompany them as a new playable character instead of vanishing. Just like in TotK, most of the Sheikah tech has vanished except for the stuff Robbie and Purah are creating, so now Lookout Landing is the new home base on the map screen and title screen instead of the Sheikah Tower.
Next we can do Chapter 9 and have it mirror Chapter 2. There can be four missions in this chapter, each revisiting the Champions and dealing with the sudden changes to their towns. So rather than recruiting them like in CH2, instead we're helping them defend their homes on adjusted maps. After this, we can move to Chapter 10. After the towns are relatively safe, the Champions reconvene at Lookout Landing and try to figure out what's going on. In doing so, Puppet Zelda is sighted heading into the Hyrule Field Chasm. CH10M1 takes place at the Great Abandoned Central Mine, and the now-friendly Yiga help track her down and expose her. Puppet Zelda and Phantom Ganon become a boss here. After this, I would have Mineru make her presence in the Purah Pad known and lead the group to their next objective; the Construct Factory and Spirit Temple. This would be CH10M2 and is how you would recruit Mineru's Construct as a new playable character.
Now it's time for Chapter 11. What I would have happen here is another four missions on brand new maps, each involving the four new dungeons and include the bosses from TotK. Mineru and Rauru lead each of the Champions back to their homes and into these dungeons. The Champions now become the Sages of this era and get a new outfit that includes their Secret Stones and a 4th weapon tier that's their Champion Weapon again but with their Secret Stone symbols superimposed behind them. Revali is a bit iffy here because he's not outright stated to have family ties to Teba and Tulin, but Revali's Gale and Tulin's Power of Wind being almost exactly the same thing seems to suggest some kind of blood connection.
Now that the Champions have upgraded into Sages, it's time for Chapter 12. Now Mineru explains what should have happened to the Zelda and the Master Sword from the main timeline. They go back to Korok Forest for CH12M1 to speak with the Great Deku Tree and free him from a Phantom Ganon. The Deku Tree is able to make sense of Mineru's story and explains that there should be a second Zelda and Master Sword in this timeline, and just like he does for Link in TotK, he helps the party find them. This brings us to CH12M2, back on the Great Sky Island fighting off hordes of monsters and Phantom Ganons to get to the Light Dragon. A more powerful Puppet Zelda is the boss of this mission, and after defeating her, Rauru discovers that the ghost of Sonia has been with this Zelda all along. Just like at the end of TotK, Rauru and Sonia's ghosts use an extremely powerful version of recall channeled through the Sacred Stone Zelda had kept, and return the Light Dragon to her previous form. This second Zelda becomes as separate new playable character that can be referred to in-game as Sage of Time, with her Secret Stone as her weapon type. Link will also get the second Master Sword, and after another powerful recall, the first Master Sword is restored, as well. Link dual wields them both as a new weapon type, and the old Master Sword and Hylian Shield from the base game becomes accessible again, too.
Sage of Time is able to realize that this is a timeline divergence and understands there should be another version of her that gets the Master Sword to the Link that she knew from her own timeline, and decides to stay here and help. Sonia ghost becomes another new playable character along with her, and from here we dive into Chapter 13, the final chapter of the expansion. CH13M1 will take place at Hyrule Castle, adjusted to account for the new split levels. This can work like the Lanayru Road map from Guardian of Remembrance where there were two separated battlefields with different things happening on them in the same scenario. The castle was suddenly overtaken by monsters and they must reclaim it. Mummy Ganondorf appears in the Sanctum as the boss of this mission. Our heroes are in trouble against him, and so Terrako does one last yoink from the future and calls Sidon, Yunobo, Riju, and Tulin from the future, post-TotK this time, in their full Sage power for one last hurrah on this timeline. Each of them gets a new outfit to make their appearance match their TotK designs while Tulin is introduced as playable. They get the Champion Weapons as new weapon types for each of them with new movesets, and to differentiate from the other Champion Weapons, we can give them that sparkle effect that pristine weapons you find in the Depths in TotK have. From here, we move into CH13M2, the final battle, in the deepest part of the Depths. This will be a highly expanded version of the War in the Depths of Hyrule phase of TotK's final battle, leading up to rehydrated Ganondorf as the final boss. Demon King Ganondorf gets to be a phase change, and so does Demon Dragon with a brand new exclusive arena in the sky for this fight, like the Blights got in AoC.
After Demon Dragon is defeated, the Future Sages return home to their timeline and the ghosts of Rauru, Sonia, and Mineru can now all pass on in peace. Sage of Time stays in this timeline in a bittersweet realization that she isn't able to return to her original timeline because there's already another version of her there. This timeline split now has two Master Swords for good. The heroes have a moment like the true ending of TotK where they all vow to continue to defend Hyrule.
Now that we've covered the story for this expansion, we need to move on to the game mechanics. I said before that Link's arm would still get jacked up so he'd still get Rauru's arm here. So how I would introduce the hand powers into AoC's format, without interrupting the runes, is I would put them on the same trigger button as the runes, but on the d-pad so that the runes can still be used on the face buttons. Similarly, we can select a few choice zonai devices to put on the other trigger with the magic rods and apples, doing the same thing. We could then incorporate these new abilities into environmental and combat mechanics, with Terrako sharing them between all the characters like he does with the runes. Rune counters and abilities still function the same as in the base game thanks to Terrako beefing up the Purah Pad.
Ascend is easy. It would still work the same way as in TotK, but it would see the most use on new maps with more verticality. Would also be good to use it on Battle Taluses like in TotK. Recall would also work the same way as in TotK; use it to reflect non-metal projectiles and also as an environmental gimmick like when enemies try rolling spike balls at you. Fuse could be used on zonai devices laying around, which I would have sprinkled throughout the maps as a new environmental thing you can do. Stick something to your weapon for a quick effect. For example, use Fuse on Flame/Frost/Shock Emitters to add a brief elemental effect to your attacks, and Fuse a Beam Emitter to shoot a beam whenever you guard for a short time. And Ultrahand would basically function as Autobuild to snap some of these environmental zonai devices together into a preset construction that will either attack enemies or allow you to traverse gaps in the map i.e. flinging yourself across a gap between sky islands, similar to how the little paraglider bits in AoC were. You would also be able to collect zonai capsules as a drop item, which then can be used on the R trigger where the magic rods are, but only certain ones, like maybe the Rocket and Time Bombs and Springs and Waterspouts.
As for the map screen, do what TotK did and make it possible to tab between the Sky and the Depths to access more points of interest. Add all the new points in the Zonai green color so they don't get lost among all the old Sheikah blues. This will give plenty of space for more stuff without overcrowding the already-pretty-full map we currently have in AoC. Also, we can make Ganondorf a new playable character (Demon King form costume included) through some postgame missions. All characters would get upgraded abilities and new moves and increased level cap, as well. And naturally, Link will get access to all the new armors introduced in TotK (including the version of the Hylian Hood with the hood down) as well as new weapons that fit in his types. Zelda will also get her starting outfit as a costume while Sage of Time gets the Zonai dress.
I want this to be DLC instead of a second game because I think the nature of AoC makes it much easier to just pick it back up and continue on, and I wanna keep all my upgraded weapons and stuff (and I don't wanna buy yet another full priced game lol). I just think it makes more sense to do it as an expansion instead of a sequel. Now, would they actually make an expansion for a 3-year-old game like that? Unlikely. I would just prefer it if they did. Like I said, I'm not saying that they're going to do this; just that if they did it at all, this is how I want it to happen. The only snag with that, though, is that AoC also sort of sets up for TotK with the Future Champions and the DLC which first introduced Tulin as having Power of Wind. I believe that the current play order to best experience the story of these three games is BotW > AoC > TotK. So this DLC expansion would then make that BotW > up through Guardian of Remembrance of AoC > TotK > the expansion of AoC. That's kinda awkward. Even so, I'd still prefer it as DLC... For one final wrinkle, I'm gonna go for the low hanging fruit and say this expansion should be named Age of Upheaval.
