Spoiler
I played through the final mission, intentionally failing stage 1, and went to stage 2 as the human path. I got the thor schematics, then it outlined green dots and told me to capture them or something. I built several thors then basically cleared the entire map from creeper, but I couldn't kill the loki thing moving around. Did I just break the scripting? It gave me free power zones though :P.
Spoiler
Read the dialog closely. It says to capture them and then TERRAFORM them to lvl 1. This will uncover some old missile bunkers that you can use to take the shields off the nexus, and then with your thor you can kill it.
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and dont forget to connect them to CN
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Wow I keep finding false bugs, thanks for pointing that out.