We get a Legends: Unova. It takes place before the kingdom splits and we're shown that the king is in control of a dragon. However the dragon only has maybe a passing resemblance to what you'd think a combined form of Zekrom and Reshiram would be, also a notable feature is 3 horns around its head resembling a crown.
The player is a new student for the castle's head magister (their version of a Professor) and assigned to a new initiative that is to tame and catalogue all the Pokemon into a Bestiary. It should be noted this game takes place just when the term "Pokemon" was starting to be used; most people still refer and think all Pokemon as beasts or monsters not really related to one another; the king's dragon is even considered a deity or holy being which exists to prove the king's right of rule. The point of the Magister's research is to prove that the "beasts" aren't all unrelated but rather all "Pokemon"; the proof being the development of a primitive Poke Ball; letting you capture the "monsters" which you can than carry around in your "pocket", a "pocket monster". The player will go around the region going on tasks for not only the Magister but for the King, the princes, nobles, other castle staff, and helping out anyone they meet while catching and researching Pokemon. But that's the basic gameplay loop, we're talking about the driving plot.
So, it'll be revealed the king is dying and his two sons are trying to claim the throne by proving themselves worthy to the king's dragon. Eventually, the king's health has deteriorated to to the point he calls upon the Princes to go on a grand quest to prove who is worthy. Some time afterwards the king is on his deathbed prompting the princes to return with what achievements they have done. The king considers them both worthy, but only one can rule so lets his dragon decide... and it chooses one of them. No splitting apart, no battles, not even a moment of hesitation, the king's dragon just chooses the one it thinks it most worthy (now between the princes leaving and returning they could have the player pick to help the princes on various tasks, so maybe have it so who the player helps out most affects the choice). The other Prince runs away furious & ashamed and shortly the king finally passes on. On the night of the crowning ceremony there's a marvelous display of shooting stars... and then a giant flash followed by a loud crash in the nearby mountains.
Next day, wanting to know what that flash & bang was about, the new king goes on an expedition along with his dragon, knights, the Magister, and the player to the mountains. Eventually the location is reached, what would be Giant Chasm, when the expedition is attacked by an icy creature, this one more looking like a Kyurem! The king's dragon battles the icy creature, and though it fights it off, the mysterious creature does something to the king's dragon resulting half of it to become black and the other half white. They follow the creature to where it fled to discover a new palace being built (the Abyssl Ruins) and the one who is building it: the other prince. The king confronts his brother and a fight breaks out, the icy creature then appearing under the prince's command and attacks the king's dragon once more. However, this time it finishes what it started to do: it splits the king's dragon into Zekrom & Reshiram (though before it did the spikes on its head shoot off) and then fuses with one of them to become a Fused Kyurem. The prince declares himself the new king now that he has his own dragon, forcing the expedition to retreat (it'll later be explained that the other prince was living in Undella Bay when the icy creature landed during the shooting stars night. He travelled to a nearby small settlement, Lacunosa Town, who told him a monster has appeared and has taken some people & Pokemon, they also starting building a wall around the town to protect themselves. Staying in the town that night, the icy creature did attack and the prince fought it off and followed it, finding the kidnapped people and Pokemon in its lair, still alive but weak & unable to move. The prince confronts the icy creature who at first lashes out but soon collapses & cowers. Feeling sympathy (and curious if its a Pokemon), the prince captures it. The people of Lacunosa swear loyalty to the prince, and soon the prince learns about the icy creature's power to absorb energy (which affects its shape). With people and a plan to get his own dragon, they all went back to Undella Bay to start building the prince's palace).
Now with a war going on between the two brothers, one with either Zekrom/Reshiram and the other with a Fused Kyurem of the other dragon's half, it's a major change. Still hoping for reconciliation and undoing what was done to the king's dragon, a peace negotiation group is formed which include the Magister and player who are allowed to travel between both territories for missions of peace and to continue the magister's research (both Princes had showed interest in it at the very beginning). The conflict reaches a new height when the Prince builds a tower (Dragonsprial Tower) closer to the King's castle (obviously Relic Castle). Using the Magister's research new beasts are made to protect both, Sigilyph for the castle and Golett family for the tower, much to the Magister's dismay as they're now turning the beasts into tools which is opposite of his goals.
Jump forward to the final battle happening in the center of Unova (where the Entralink is now located, before just all a dense forest initially left unperturbed as a "Beast Sanctuary"). The King and Prince have their final clash where it looks like the King is about to lose, but then suddenly three Pokemon bearing the crown horns come in with an army of Pokemon to help the King, the Swords of Justice (btw it would be the Magister and player who went around finding the Swords of Justice and convincing them to help). Still, even with their help the battle is dire, the King's dragon is injured leaving the King to face (a weakened) Fused Kyurem alone. But that's when the King revealed a back-up plan: two circular stones & a monochomre spike. Stabbing Kyurem with the spike (the DNA Splicer), it activates and the King pulls his dragon into one of the spheres and the other half of the dragon out of Kyurem and into the other, forcefully changing Kyurem into the form we know it as. The Swords of Justice fight Kyurem shattering most of its body though it releases its remainder of power into a Glaciate to escape, the Prince also vanishing along with it.
For their help, the King declares all the beasts to be living beings. However the damages done to the King's castle (an attack by Kyurem slowly turning the area into a desert) and the Prince's palace (it's unstable foundation sinking it beneath the sea) leave both unsuitable to rule a kingdom from. And with how much harm him and his brother has done, the king decides to let the people of his kingdom rule themselves while he stays in the forest to rebuild the forest and watch over all the region, the Swords of Justice joining him. Post game would start with everyone moving to a new settlement: Opelucid City. The King's dragon's orb would be hidden in Relic Castle, the other orb would be placed in Dragonspiral Tower, and the DNA Splicer kept in Opelucid. A final thing we learn is the people who followed the Prince had "surrendered" and became subjects of the king. They all return to the abandoned Lacunoda Town and finish building the wall in fear of the prince & Kyurem returning for revenge, telling their children of the monster of Giant Chasm as a way to keep them from wandering there. But, before they abandoned the sinking palace, they
wrote a legend of the king and left it in there: King defeated Kyurem alone. The Swords of Justice joined King in a day. King called Beasts (Pokemon) beings. King is hope and future. The great King Harmonia.