Unfortunately this isn't like making a fan fiction, if you take from a novel or whatever you're following and use it in your piece, it's okay as long as it's free or you get copyright permission.
When it comes to ripping content from a CD, you're not allow to do that in computer games, for whatever purpose, it's still illegal and a bad idea. You can use their characters if they don't let you use their models in their end-user lisence (some do, as there is a modding community) then you have to model them yourself.
Even then making a fan game is risky, if the company find your game, they can ask you to cease making it or giving it away (possibly if they see it as a thread to sales, or misrepresents the company)
A lot of people make fan games, but ripping from a CD is not a good idea.
Good luck with your game by the way, for 3D modelling, check out a couple of tutorials from my website:
http://www.seppuku-arts.co.nr
I haven't updated my new tutorials yet, I should have at least 2 useful ones.
Exit Pursued by man-bear-pig