Woah, I didn't know we had one of these!
Here's what I was thinking for the terrorist commanders plan, and what I've been setting up. The terrorists plan to use the base's technology to create an Einstein-Rosen bridge, a sort of "tunnel" to an alternate dimension. Their hope is that the terrorists and scientists from the other dimension will have weakened each other so much, that they can sweep up the pieces and own the parallel-universe base.
The reason they're trying to capture Lockdown (the prisoner from cell 8Z in the sublevels, who doesn't appear to have powers) is because his power is actually to transform matter into antimatter, a crucial phase for the bridge.
Things I've already included to hint at this plan:
1. The commander tells Hans to supervise the transport of large concave mirrors. Those are the framework for the bridge.
2. He describes Lockdown's power as "transmutation."
3. He actually calls it an "Einstein-Rosen bridge" in dialogue.
I was thinking that they need control of the AWTR because some of the experimental weaponry is necessary for the bridge to work.
Serris, if you had anything else planned for the terrorists' master plan, this one could easily be shortened to just a secondary plan, or the real plan could be put into motion by an ambitious terrorist lieutenant, who siezes control once the Einstein-Rosen bridge is destroyed.
What does everyone think?