The two boys have an incredible secret that they don't even know: they are Pokeumans, a group of species that are born human but turn into Pokemon between their teens and twenties. Link has come to Reality to learn from L why he can't take on his fully human form anymore, just to find that L is in the same boat. They flee San Antonio after a sleeper agent (people who don't know it, but are armed to kidnap Pokeumans when they find them) is alerted to them. If L is right about their condition, their best chance seems to be in Denver, where a base for those like them is.
If you don't have a clue about Pokeumans, I recommend going to Ryusuta's profile on DeviantArt.com and reading her books 'The Story of Cubone 1-3', and by going to the group in it's description if you're still confused.