I have another Pokemon one!
In Gold/Silver, you play as a freedom fighter who is trying to gain the Johto region's independence. You see, not only was Red/Blue set after a war, but so was Gold/silver. In the few years following Red/Blue, Red and the Kanto Pokemon League, led by Lance and Red, decided to attack Johto and conquer it. The Johto army managed to hold off the Kanto attack for a while, even pushing into Kanto and claiming some territory. However, the Kanto government reclaimed its territory quickly after the Johto army invaded. They pushed Johto's troops out easily with tremendous force. The Johto Pokemon League surrendered and disbanded before the Kanto League could launch an offensive that could have potentially obliterated Johto. This explains the lack of a Pokemon League in Johto, as the Kanto Leagues assumed control over Johto.
The resulting war was swift but costly for Kanto. While Kanto succeeded in taking Johto, they had some casualties. Battles in the Pewter City region had destroyed the Pewter Museum of Science, the Pewter City Gym, and had burnt down Viridian Forest. However, after the war, Kanto citizens used Grass-type Pokemon to restore the forest. However, the best they could do was restore it in a lesser state.
The Johto League also surprised Kanto by flanking from the east, and attacking Lavender Town. The battles for Lavender were fierce. The Pokemon Tower was destroyed in the fog of war.
The Johto resistance was desperate near the end of the war. Attacking Kanto from the south, they briefly seized Fuchsia City, seeking to gain supplies from its port, and more importantly, the Safari Zone. Johto fighters thought they could obtain fresh supplies of powerful Pokemon from the area. However, the the Kanto army regained Fuchsia, and the Safari Zone was destroyed in the process.
The Safari Zone's warden, nicknamed "Slowpoke" by the locals, fled the area at he first sign of Johto rebels. After the war, he set up his practice once more, this time in an isolated region of Johto where nobody from his old life would bother him.
The war theory also explains why nearly everybody in Ecruteak City has an obsession with the story of Ho-Oh. Ho-Oh is seen by the Johto populace as a definitive symbol of the region, and an ideological rally point in the face of Kanto imperialism.
Furthermore, it explains the reason both why Red is in isolation at the end of the game. He, only 13 years old when you find him, feels extremely guilty over all the the destruction he was a part of. he can't face himself in civilized life anymore, even though the people of Kanto hail him as a hero.
Also, it explains the huge presence of team Rocket in Mahogany Town. Mahogany was a small Town, yet the Rockets set up a huge base there and performed experiments on the nearby Lake of Rage. The authorities had to have noticed the large number of Rockets there. And notice they did. The local Gym Leader, Percy secretly made a deal with the Rockets. He would make the town turn a blind eye, in exchange for the Rockets building a force of Gyrados large enough to challenge Kanto once more. The Rockets, however, had no such plan. They were instead focused on rebuilding enough to attract Giovanni again. Both plans failed once the player's character in Gold/Silver came to Mahogany and wiped out the Rocket base.
Additionally, it explains why Professor Elm set up his own laboratory in Kanto. Elm is by far the youngest Pokemon Professor to date, and clearly the most inexperienced. Elm was also originally a disciple of Professor Oak. However, when the war began, Elm quit working for Oak and fled to Johto over political differences. Once the war ended, the two reconciled.
Your character in Gold/Silver realized the potential power one could have if they become Kanto league Champion. Your character figured that if a Johto citizen could take the control the League, that person could negotiate a split between Johto and Kanto without bloodshed. However, after failing to see that happen one you become Champion, your character thinks that beating every Kanto Gym Leader would be the solution. This plan also fails miserably.
Finally, in a fit of rage, your character sees the futility is his/her plan and takes their anger out on the one person left that they can: Red. Red, face to face with the one person who fought so hard the reverse the evil committed by Kanto, fled after the battle, never to be seen again.