As far as I know, when Michael was in surgery he had visions of Charles Westmoreland and uncovered what Scylla actually was? Or did Michael use his extraordinary brain to know the reason behind SCYLLA?
Vision of Charles Westmoreland was yield of Michaels imagination, so however you put it it ends that Michael figured out scylla by himself.
Up to this vision, Michael never actually thought what scylla really was. Don Self told him it was the black book for the company so Michael assumed that it was, that is the power of suggestion.
After Don Self betrayed them, Michael realised it was all a lie so scylla could actually be something else. This was also the part where Charles "told him" "Things are not as they seem".
Now curiously Michael pulls all his information about scylla in attempt to figure that out. Words Bargain and Power stood out as they were mentioned few times... Which seems was enough for Michael to make his own conclusion about Scylla.