Interesting. And interesting plot twist.
Actually, there's been a fourth cloning facility. It is mentioned in Perpetual Doom that there is one in thedude's base, which the Knights destroy.
I have to admit there are some things in this chapter that when combined left me annoyed. For one thing, the fact that C.O.D. (which you still refuse to write whole :P) has Omni in its name doesn't mean it's also omniscient (or omnipotent for that matter). For another, I don't like the representation the Paradox Rogues and the Nexus Force get in this chapter. Remember that thedude's army posed a serious threat to the Nexus Force, took over several kingdoms and maintained rule over them for quite a long time. It's not exactly what I'd call incompetent. And the fact that kids played Lego Universe doesn't mean the Nexus Force consists of kids. Any LU story that wants itself to be considered realistic should consider it a stretch to have only a small percentage of the Nexus Force to be around 14-16 years old. I don't care what other stories did or what Great Minifig Missions said, but it just won't do. Lastly, I must say that James is a know-it-all that wants to be always in control of the situation and it's starting to get to me. Then again, that could be considered a good thing... if that's what you want to do with him.