Enables starbases to be the flagship of your ships
I believe this is just a figurative speech...
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Omygosh, I think you're right. How did I miss that? The thing is, they throw this word "flagship" around as if it means something ... and it *could*! That's what kills me. They have this silly little goosed up scout ship and they call it a "flagship." It oughta do something more dramatic with a name like that. Like you could install an inspirational captain at the helm (okay, I'm thinking of Jean Luc Picard, I admit it) who could give a fleet extra power -- you choose militaristic, influential, or ... Or no, wait wait, your flagship could gain reputation which would preceed it. You could send diplomatic missions to other planets and have a better chance of establishing an alliance. When the flagship levels up (via battles or found anomalies) its reputation would increase, further helping it in both battles and diplomatically. I guess it would be your "hero" unit, to steal an idea from Warcraft...