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Either you ignore the SUs completely or figure out how it interacts with a self-modifying ship. One of the issues in 'building' Gomtuu, or any bioship, in regards to SUs is that living things are built through growth. Similarly, they can adapt to changing circumstances by modifying themselves at a structural level. Taking Gomtuu specifically, it was meant to carry a crew, but lacks one—but we saw it modify its interior space to accommodate Elbrun very quickly. Maybe its size is dependent on its compliment, as it expands to accommodate more? Could it grow on command to accommodate more bulky cargo? Has Gomtuu been 'eating well' during its depression? Maybe we're seeing an emaciated, shrunken version of Gomtuu, much smaller and wrinklier than you would see of a hale and hearty member of the species.
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I have been thinking about the secondary weapons system, you could treat it like a modified Romulan Plasma torpedo weapon.
Plasma Wave Generator (Gomtuu can generate 1 pulse wave per round)
Arc 180 degree's propagates from the vessel at .99c.
Base damage 1500 (to all vessels/targets caught in arc) out to 1 MU (30,000km's) power 150/sht
Dissipates at 6 damage/1MU
