Phoenix was never meant to restart the Project, they are just the best ones immediately available. My assumption was always that Phoenix would take control of the Project only until they could wake the regional commands and/or "Second Base" and turn control over to the administrators suited for the job.
And Prime Base does not exist in isolation. Yes, the location needs to remain secret (Why I have always advocated for limiting its scope to those activities requiring a minimum of traffic), but the only reason to abandon it is if the rest of the Project is so deteriorated that it cannot be revived. Otherwise, keep it secret, revive the rest of the Project, and get to work!
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