We do know Obama (like most presidents) is pretty cozy with the Intelligence Community. We know Trump isn't. I think a coup d'etat or shadow government is too much of a stretch, but this may at least let them work around Trump to an extent.
Also, we're living in interesting times where thoughts like "the intelligence agencies are covertly trying to work around the President!" are actually considered a neutral or good thing by many.
Trump and those sympathetic to him could easily use the power of the intelligence apparatus to punish anyone who opposes him. We've already seen Congress pass a measure allowing them to reduce any federal employee's salary to $1. There's also a bill that would make future federal employees at-will hires that the president can fire. Imagine the climate of fear and intimidation that can be created if the president can fire anyway and has access to a massive surveillance complex that monitor all manner of digital communications.
Now maybe Obama knows something we don't, maybe he knows there really is damning information about Trump out there that just needs to find its way to the right hands. But even if that is the case, a more powerful surveillance state is not going to police itself, nor weaken itself even if Trump gets pushed out.
Makes no sense. If he did, a couple of months ago would have been the best time for it to come out.
All things considered I think there's a decent possibility that President Trump has more skeletons in the closet that haven't been outed yet.