You know, Hubris is probably the Occam’s Razor explanation. NSA probably said OK Hillary, we ran a line to your house that taps Trump’s stuff, do with it what you will. Pagliano hid it away from the other servers in the ‘office’, grabbed data, and used it as a backup/mirror server for the email servers upstairs when it went croaky and never removed the mirror.
Then it all went haywire from there, and Pagliano took the 5th because NSA strongly counseled him to.
I’m not sure where Loretta Lynch fits into this, but I recall she scurried to give immunity to lots of players. She’s gone full-blown anarchist now, calling for blood in the streets.