This is pretty fun, I have reached the point where the compression core says protocol 2 is needed, and it looks like there are more nodes on it so I assume there is more to the game, but I am stuck. I have made the overdrive overheat, and tried clicking everything, but I see no more. Please help! Overall though I like the concept of this game, I would love to see if there are more parts to this machine, and maybe more things to interact with? Pretty good game though!
-EDIT-
I realize now looking at some of the description stuff that there may not be a second protocol, as it says one complete protocol. I also think as a way to keep going, you could make the distribution matrix as a slow upgrade chain, each option slowly upgrades one thing, so overtime you can focus one or the other, or have them both upgrade at the same rate. Just a thought as it feels a little odd and out of place right now.