The funny part (well, *a* funny part of a rather funny game) is that nobody in the game is named Charlie. The ninjas are named Roy and Lon. Instead, it's the name of the character designer, Charlie Arai.
I do not like that ninja, his smug aura mocks me Also, Freddie's face kinda reminds me of Nern from Lisa the Painful. What with the mustache, nose, and eyebrows
Here are guesses for why the bosses are wanted. Blues: outlaw related crimes in the modern world. Sanders: being a rogue general. Freddy: sexual assault against straight people. Bear: dangerously cheating. Dr Mac: probably world domination.
I'm thinking that Bear and his football team might have also been illegally squatting in the football stadium, which appeared to have been abandoned, with the way that they used it as their hideout.