I have like way too many ideas, most of them involving some kind of civil war. Lets see:
You are a minor lord in a strategically important region in a kingdom embroiled in a civil war. You must choose between the loyalists, the rebels, or using the opportunity to declare yourself independent. When siding with either faction the leader of the opposing faction will slowly become more extreme and desperate, even seekng help from a rival kingdom that uses the invitation as an excuse to invade. You have to defeat both the enemy faction and the rival kingdom to win the game. In the independence route, you are the one who has to go to extreme lengths to survive all alone against the two big factions, and you will be the one requesting the rival kingdom for assistance. After defeating both factions you know have to betray your ally since they are also a threat to your independence, this will include betraying and killing a previously playable unit.
A civil war plot where you start at the loyalist side, but switch over to the rebels when the king gets too evil for your tastes. Then later on when the rebel leader gets too ruthless you split from him too and start your own faction. There will be an optional unit locked behind a really hard side mission. If said unit is recruited and survivves all the way until after the Endgame where both enemy leaders are defeated they will go "you followed the king until you disliked what he was doing. Then you followed the rebel leader until you disliked what he was doing. Now I dislike what you are doing.", and betray you over some ideological dispute. This will lead to a really hard Endgame-x chapter where you defeat the traitor but spare them because you realize there has been enough of people turning against each other, and as one of the main culprits behind al lthe mistrust you need to take responsibility for your actions and take the first step towards people working together instead.
A successsion crisis where the two royal siblings/cousins love each other but end up used as figureheads by the two enemy factions and thus have to fight each other. They generally agree with their faction's ideals, but they have no real political power. The setup would be an Alm/Celica thing except the two parties are on opposite sides of the conflict. The final chapter has the royals and the faction leaders fight each other, and you have to choose which side to play as. The stated objective is to kill the opposing royal, but there's a secret objective where if you kill both faction leaders (one of which is a playable character) and have the two royals face each other they decide that they don't want to fight each other and you unlock the secret golden ending.
A three routes game where each route plays differently, like Birthright/Conquest but even more drastic. The routes all take place simultaneously and the protagonists of each route occasionally meet or mention each other. One route follows the leader of the alliance that's fighting against the evil empire. The campaign is Genealogy-style and every unit fights with a massive army. The second route follows the prince of a vassal state under the empire hoping to gain freedom for their country, but unable to fight the empire directly as things currently stands. The campaign is classic linear Fire Emblem and every unit fights with a battallion of troops. The third route follows an oracle who's recieved a vision of a terrible calamity that will seemingly be caused by the evil emperor and sets out to stop it. The campaign is Gaiden/SoV-style with a world map and dungeons, and every unit fights alone. At one point the alliance leader will fight the vassal prince. In the former's campaign this will be depicted as a single fight between two units but in the latter's it will be an entire chapter. Similarly the vassal prince will fight the oracle, which is depicted as a single unit vs unit fight in the former's campaign but an entire map in the latter's.
A game where you play as an old mercenary captain tired of constant war who wishes to build sometihng that will last. The game starts as the big empire collapses, and you are tasked with defeating the rebelling citizens of a city on the empire's borders. But you join the rebels instead, become a king ruling jointly with the city council, and your old mercenary company now becomes an order of knights. The earlier chapters has you fighting bandits and loyalists, stopping an invasion from a neighbouring country, and building up your new country, until you start making contact with various other secession leaders and form an alliance against the empire. As you finally defeat the empire and take the capital the most powerful member of the alliance betrays everyone else, enacts a giant massacre in the imperial capital, and starts trying to refcreate the empire with themself as the new emperor. While the alliance goes to face the new emperor you have to go and deal with the neighbouring kingdom from before who tattempts a second invasion, and are thus away while everyone else gets absolutely assblasted. With the other leaders dead or massively weakened, you become the de-facto alliance leader in the war against the self-proclaimed emperor. The chaos that follows the disintegration of the old empire gives room for lots of side missions where you liberate cities from bandit kings or defeat imperial remnants still holding on after the fall of the capital. The borders between the various states will constantly change on the map as the war unfolds, and these side missions will permanently add new cities and regions to the borders of your fledgling kingdom.
An idea I thought up while thinking of how good a job Warcraft 3 did of leaving on a world that was completely different than what it started with. You start as a mercenary captain aiding the good ruler of kingdom A against an invasion by the rival ruler of kingdom B. The twist is that kngdom B wins and you have to flee with the now incognito A-ruler. Ruler B will have to withdraw however when their army catches a plague, and this plague also ravages kingdom A, making tihngs even worse than they already were. In this chaos, a self-proclaimed prophet who showed up earlier but no one paid any attention to will start gaining followers, and the new religion C-brethren will start rebuilding kingdom A. Meanwhile the party takes refuge in empire D and eventually has to defend a border city from an invasion of C-fanatics (not necessarily endorsed by the prophet, since the kingdom is still something of a chaotic mess and the whole religion is kinda loosely organized). The party defeats the invaders but the citizens wonder why the emperor didn't do anything and start to wish for independence. Meanwhile several imperial princes are actually converting to the new religion, and even the former A-ruler converts, since this prophet is clearly doing a much better job of leading and rebuilding the kingdom than they ever did. These new converts are causing the emperor, who has strict rules against other religions, to start cracking down with the imperial army. The convert princes fight back, and now even unconverted princes start proclaiming independence as the emperor weakens. In the end the emperor is defeated and has to acknowledge the independence of the revolters as well as introduce freedom of religion in what remains of the empire. The Ruler of kingdom B either dies of plague offscreen or shows up as an allied unit in a battle against the D-emperor or the C-fanatics who you can "accidentally" lose to enemy forces. I only now realized that this last idea takes a lot of ideas from the previous story.