We can't decide on what to do with one of our villains. He is an outlaw Flygon that has escaped from jail, that had a life sentence. He is a thief and also a murderer. to make a long story short: our character Ben (an old Ampharos) used to be on an Exploration Team with his father when Ben was a Mareep. Bens father recieved a letter telling him about a nasty outlaw on the loose known back then as Vibrava, and knowing the risks of taking his young lamb to fight a high ranking outlaw with him, decides to go alone.
Ben decides to follow him anyway, seeing as they've ALWAYS done missions together, and goes into the Mystery Dungeon after him. Bens father confronts Vibrava, and they fight for a long while, until suddenly Vibrava evolves into Flygon! Flygon beats up Bens father, and makes him crash into a wall. Ben comes into the room and sees his father in trouble, and calls Officer Magnezone on his Exploration Badge for help. Flygon, not wanting any witnesses, fires off a Hyper Beam at Ben! Bens father pushes him out of the way and takes the Hyper Beam for his son. Ben is furious! So he tries his best to fight Flygon as best he can (Tackle spam!) until the police arrive and arrest Flygon. It's too late for Bens father, and after teaching him a very powerful but also very risky Dragon-type move (Outrage) and saying goodbye to Ben, he dies.
Ben gives up being an explorer soon after this, and lives alone for several years, eventually evolving into an Ampharos. But then, just when things were looking up for him, with a new friend, everyone reunited and happy, and the world saved, someone comes to crash the party. Flygon escapes from jail! Ben finally has his chance at revenge and goes after him for a final showdown.
Just to spoil you guys, Ben survives. But what to do about Flygon?
We can't kill him, or have him kill himself. That just doesn't seem right.
We can't throw him in jail for obvious reasons. He'll just get out again.
We can't make him turn good or suffer amnesia. He doesn't deserve mercy after what he did.