Honestly, I didn't think that people would still be interested in this idea at this point in time, So I never thought through the details that much.
Well, anyway, I always pictured the protagonist as a guy. If it's not possible to code in a male character, though, we can certainly go with a female. Either way, let's call him 'Zeta'.
The villian should be a User, I think, just because an instant routing engine is something only a user can make. Let's say that his name is Freddrick.
Hmmm... Boss battle. I'm kinda stumped on that one. Maybe something to do with breaking the Users connection and contacting the authorities.
I've just had a thought. Programs aren't really known for taking the initiative on things, so maybe another program can come in at some point and get the 'attempt escape' ball rolling. Kinda' like Wheatly, only more competant.
As for portal walls, I'm thinking either something to do with red and blue circuits lines, or just straight black walls for non-portal and grey for portalable.
I better start working on puzzle ideas if we're actually going to try this.