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Sure. I imagine they would be much like that ship on Farscape. FTL travel might be a bit of a snag.

Not possible as the setting is presented, biotech is just too undeveloped. A few hundred years in the future maybe but they'll need to either disable the NEXUS or find a way around orbital defenses.

That could be were the setting is heading, as one of the rumors about the Seedlings suggest that they might be giant space craft that are gestating inside the planet.

I personally like this rumor, as I can see it as a Liberian plan to permenatly defeat N.E.S.U.X. When all the Seedlings finally mature, they begin a coordinated launch that not only destroys the planet, and the machines with it, but also takes all those living inside them to another planet to colonize (or maybe they all go to different planets).

This gives me some ideas, and helps shape a few ideas i already had.
Drop the nanite plotline completly though.

Living Seedling/Warmount Space Ship -- Check
Bio-Shuttles Shaped like Bugs -- Check

Living Symbiotic Armors (Dreadguard or Old Riathenor like) -- Check
Bio-Weapons -- Check

This makes me smile

FTL Travel could be as simple as it is in Farscape. Star Burst ability.
Sit back, rechange the StarBurst ability, then repeat.