Indeed...the only thing that remains is the "black alert". Remember when Tilly seemed horrified, reacting almost like Pavlov's dog, every time hearing the black alert and freaking out? Now she's all up in the spore tech - basically running the whole show during Stamets' absence - and doesn't even break a sweat. That's more than just character growth, that's an internal reboot from the original core plotline.I agree. S31 is a shadow organization. They would not advertise their existence with badges. This was clearly shown to be the case in DS9. Maybe the original idea of the black badges was that the Discovery was part of some top secret department in Starfleet that tests new technologies like the Spore Drive? But clearly, the idea got dropped.
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