It would start with one of the professors approaching you (I prefer the original so lets say Oak).

Oak:Excuse me are you a Pokemon Trainer?

Trainer Choice:yes, no
                                                                            if no
Oak:Oh I assumed you were because of the pokeballs okay sorry for the inconvenience.

                                                                            if yes
Oak:good I need your help, you see I've been getting reports of dragon pokemon running rampant from every region including here in Miryus. They have been attacking people and cities. So I have been asking trainers to go to specific cities and protect them, can I ask you to go to (insert city name)?
Trainer Choice:yes, no
                                                                            if no
Oak:Please they really could use your help.

Trainer:Fine I'll go.
                                                            Quest continues from there
                                                                           
                                                                            if yes
Oak:Thank you for your help, I'm sure the people of (city name) will be grateful as well. Oh and while you're there if you find anything that could explain the dragon pokemons rage please tell me about it.

You go to (city name) by any means of transportation you can. Once there you will need to battle 10 dragon pokemon all in their final stage of evolution (you will not encounter any Dragonite or hydreigon). After battling 10 dragons you will be approached by a man in a white coat.

Scientist:Excuse me but I could use your assistance would you follow me to my lab.

Trainer Choice:yes, no
                                                                            if no
Scientist:Please you have to help I don't know what else to do.

Trainer:Fine what do you want.
                                                           Quest continue from there
                                                                            if yes
Scientist:Oh thank you, please follow me to my lab.

He takes you to his lab which is located at the base of a mountain. He then explains why he needs your help.

Scientist:Recently I conducted some research, I wanted to see why some dragon pokemon are peaceful like Dragonite well others are chaotic like Hydeigon. I was unsuccessful so i decided to conduct an experiment to see if these personalities could be switched. I started with the Dragonite and the experiment was a success or should I say failure,the Dragonite ceased to be peaceful and caring and became chaotic and destructive. Unfortunately in the Hydreigon's case the experiment was a failure,he showed no signs of a personality change and continued to be chaotic and destructive. After the experiment the two pokemon escaped and as you can see destroyed my lab, also there were some items missing I believe they took them. After escaping the two pokemon headed for the top of the mountain. Originally I was going to deal with this myself but I don't have anything to subdue them with, and then I heard the news about the dragon pokemon so I decided to look into it. I discovered that there is a reason Dragonite and hydreigon act the way they do, it's because they are the balance holders. Dragonite peaceful and caring represents good, and hydreigon chaotic and destructive represents evil. By removing one from good and placing it in evil but not doing the same for evil I inadvertently threw the dragon pokemon out of balance which has obviously enraged them. So I ask you please help me retrieve the pokemon for me so I can bring things back to normal, I will of course compensate you.

Trainer Choice:yes, no
                                                                              if no
Scientist:What but you have to help.

Trainer:No find someone else.

You leave and go to oaks lab and tell him of your findings, he thanks you and gives you your reward. 200poke 100xp
                                                                        end of quest
                                                                             
                                                                             if yes
Scientist:thank you so much you don't know how thankful I am. There is a door in the back that will take you to the mountain.

You go to the mountain and after a few obstacles and battles you reach the top where you find the Dragonite thrashing about but no Hydreigon. As you walk towards the Dragonite the Hydreigon appears from the sky and attacks.

Hydreigon Move Set:Earthquake, Dragon Pulse, Screech, Double Team. Item:Leftovers
Explanation:Two moves of good attack and accuracy, a move that lowers enemy defense to do more damage, and a move that raises the users evasiveness to make it harder to hit as well as an item that gives the user HP back each turn.

After defeating the Hydreigon you walk toward the Dragonite until he spots you and attacks.

Dragonite Move Set:Dragon Rush, Hurricane, Blizzard, Thunder. Item:Wide Lens
Explanation:Four high power moves with low accuracy and no negative effects on the user and an item that raises accuracy to nullify the low accuracy.

After defeating the Dragonite you go back to the scientist and tell him what happened.

Scientist:Thank you for your help it is much appreciated now, if you'll excuse me I must retrieve the pokemon from the mountain. 200poke 100xp

You then return to Oak at his lab and finish the quest telling him what you found and what you did.

Oak:Thats quite a story, thank you for helping to save the dragon pokemon. 200poke 100xp
                                                                  Total quest earnings:400poke 200xp

I am new to writing so any type of feedback is much appreciated.
I've noticed that my comments have seemed a bit hostile but I don't mean them to be I'm just trying to explain things in greater detail.