I think I read somewhere that it doesn't but I would just like some clarification.
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Perhaps Blue have been tasked with something of importance, but different to the Infinity's mission. They could be, along with the SIII's, forming a unique unit of their own -- for highly ambitious and dangerous missions. Perhaps they are looking for the ONI vessel from the last chapter of Primordium. They could even, and I realise this is all speculation, be looking for the Librarian.