Grimm Fandango said:
Just so we can clear this up, at the end of season 2 when the General said something about Michael doing "what he was born to do," was that in reference because Michael's father was in the Company at one time?
It was after Michael was captured and sent to Sona. The conversation went closer to the lines of:
General's Underling: You know he'll just break out, right?
General: Of course. It's in his blood.
That "in his blood" line seemed to spawn a lot of speculation that Michael was some sort of genetically engineered super-genius, but I always just took it as a remark about how he'll be determined to escape, because it's just the way he is.
Now, with what they're doing this season, they could be angling towards Michael being "planned" in some way. The remark that the doctor had seen a tumor like that before (which seemed to imply Michael's mother), the implication that Aldo was more involved in The Company than was previously known, etc.