>>136159507You beat the final gym, and go to collect the reward, when the secret police start to hunt you down. You may be stronger than them, but they outnumber you, so you're forced to run. With the government searching for you, the rebels attempt to revolt, and the country turns into a war zone again. The capital is totally fortified, however the government is losing ground and the rebels mostly take over the countryside and smaller towns.
At the end of the game, you lead an attack on the capital, and end up fighting the dictator, who has some new legendary pokemon. You win, and he dies from an attack from your pokemon. As the rebels cheer, you search the capital and end up finding your dad, who's old and weak now. He tells you how proud of you he is, and dies. You end up living happily ever after with the girl companion, and the region returns to normal.
The end.
Of course, that was just a mock up.
There would be larger regions, a better story, and realistic characters.