In the previous episode, the writers dropped the revelation that the Company might be doing terrible, immoral things for all the right reasons. That gave me hope that the Company might be recast, ever so slightly, as more nuanced in their actions and motivations. I'm not sure that this episode did much in that regard, and it might have even undermined the best aspects of the plot twist. (Never mind my annoyance with Michael's remarkable lack of bandages, wounds, etc.)
The thing about giving villains a meaningful rationale is that you must, inevitably, explore how that information pertains to the decision-making process of the character. Much like Gretchen's motherhood gave scope to her actions, the truth about Scylla and the Company's true purpose should serve to explain the General's actions. It's not about humanizing the General; it's about making him more than a two-dimensional figurehead for "the bad guys".
For that reason, I had hoped that Michael's discussions with the doctor in this episode would have been more about defining what the Company really is and why they employ their decidedly sinister methods. Frankly, trying to turn Michael with talk of his mother might play into the final arc of the series, but it doesn't make much sense. Michael is all about subtle logic and the big picture.
So wouldn't it have made more sense to appeal to that logic and justify the past as well as the present? Michael may not trust the information completely, but it would be better than trying to appeal to him on an emotional level. That just serves to remind him of all he's lost and stands to lose. The trick was taking his emotional reactions and casting them in a new light, to emphasize why the ends justified the means.
Lincoln's side of the equation was a bit more compelling, because his motivations make sense. It also didn't hurt to have a more complicated dynamic at play with his "team". I'm very happy to see Mahone as Lincoln's ally. Oddly enough, I'm sorry to see Gretchen go as well, and not just because I think Jody Lyn O'Keefe is ridiculously hot. I think the character was a constant reminder of how evil the Company can be, given how completely they twisted her over the years.
The purpose of this episode was somewhat obvious: to set Michael and Lincoln against each other, with their mother in the middle. It's a bit of a hard sell, because while Michael now has reason to side with his mother in the long run, Lincoln has yet to be given strong reasons to back the Company. Maybe the next couple of episodes will clarify those motivations and make up for the lack in this installment. With only six episodes left, however, I fear there may not be time to capitalize on everything this season has offered.