2 - Stemming right from the first side-quest, the old hermit would ask a favor of the player; To go down the mountain side to check and see if any damage had been done to the surrounding area below. He'd go himself but down below is a valley filled with some unruly Pokemon, far too much for him and his own Pokemon to handle in their old age. Moving down the side of the mountain can be done in different ways: Ledges, maze of sorts with ledges along the way, etc. Suggest that it be made with a script where the player can find Pokemon even outside of the grass.
Upon reaching a higher ledge on the mountain side, the player would hear much commotion coming from the base nearby - Sounds of angry roars and of a man's yelps of fear. Making their way to where all the commotion is coming from, the player would find a ruin-maniac/professor/etc being chased by [insert Pokemon here]. This NPC decides to run passed the player - Leaving them to deal with this infuriated Pokemon. After a battle ends, the NPC returns to speak with the player. Letting them know he/she had been watching, and that they apologize for what had just happened, begging the player to let them explain why what occurred did.
The NPC explains they were in search of some ruins they believed to be in that area, but when they had tried to find it, the side of the mountain burst open and a bunch of water had come running down - Filling the valley a day ago. Due to the incline that it had, the majority of the water continued down through the valley. This NPC shares of how they had explored the cavern above late into the night, only to leave it exhausted. They made it down to the valley to take refuge in a cave where they had awoken a rather large Pokemon moments before the player had heard the commotion. After explaining that, the player asks why they had thought a ruins was located in the area - At this time the NPC pulls out a map, and shows the player. The player takes the map from their hands and turns it right-side-up - As the NPC had misread the directions completely.
From these two side-quests, the player can later meet up with this NPC to help find the ruins they've been searching for, as well as explore it, even find a secret or two hidden within. Can have some mythical Pokemon laying below that can only be awakened by the music of the Pokeflute - Why? It was made by this very being and is a key to even get to it. In order to get through certain area's, the flute must be played. Can have the player find the ruins earlier into the game or some time later on - Whichever works for you. Can have a bit of backstory as "This particular Poke-flute was passed down through the generations of Mr.Fuji's line, etc etc...". When it's needed or if this idea fits at all with your personal plot, I'll type a more detailed background than that of course.
In order for me to do any starting ones, I need to get three questions dealt with: Is there a specific 'why' the player doesn't know of gym's or the league? And how was it kept from them? The league would have coverage in the news, TV, travelers, school, etc. And could you go into more detail about the starting town? The introduction is a bit...mashed together, some parts don't make sense at the moment:
Mystery of the Pokeflute through reds adventures (yes they coming back) It was lost on a ship of cargo that were stolen by some grunts to hear there is a base where sightings of cargo being moved into the ofrst by your (in) your home town. so decide this is your mission to help the town, it was always your dream to get into the paper. You know that to defeat these grunts you were to have a Pokemon, the only man you are to know who can give you these are the professor in your town professor "insert name here" on entrance to their lab the professor is not there, an assistant comes to say he went to conduct research, he has been on an all adventure going to the summit of the volcano into the dense underbrush swamp and now he is in the lake in this town. go find him.
Fixed some spelling and some of the grammar above, but the phrases/words in bold kinda need some explaining. The typo "ofrst" is to mean 'forest', but the rest of that sentence doesn't speak of where the town really is. Is it inside the forest or just outside of it? You also go right into saying how the player looks at the Snorlax, but how? Is it in the paper they had gotten or is it close enough for the player to see, just outside their town? And the bit that has an underlining just confused me in how you described the starting mission/goal. As a feature you explain "old hero's return" and "evil teams return", which doesn't make sense to really put that bit within the parenthesis there at all.
And the player does know about gyms and the league but its not like those things really intrest him (well until he ends up having to battle)