The past few episodes, both before and after the hiatus, made the claim that Michael was just like his mother. In other words, Christina is just as much a genius as her son, which means that Michael may have met his match. This episode is all about how clever Christina can be, and as it turns out, she's pretty damn clever. Michael hasn't had the opportunity to use that talent in a long time.
Christina manipulates Lincoln, Michael, and Sara so well that it distracts from any thought that the whole thing doesn't make a whole lot of sense. Christina's plan is supposed to have been set in motion a year earlier. That's roughly around the time that Michael was doing his best to get Lincoln out of a death sentence for a crime he didn't commit. So was Christina responsible for the gambit that promised to put a Company puppet into the White House, and thus responsible for sending Lincoln to the gallows?
Considering that she was willing to place Lincoln right back in the same position in this episode, I would think that she was behind much of the Company shenanigans from the start. And one can see why Lincoln's true origins, and Christina's disagreement with his inclusion in the family, would lead her to use him as a patsy time and again. From that perspective, it makes a certain kind of sense.
From nearly every other perspective, it just feels like a huge plotting mistake. The fact that Michael and Lincoln are brothers has been at the core of the series since the very first episode. Undermining that sounds like a great twist, but it would have been a lot better if it had been a calculated ruse to keep Michael from running to Lincoln's aid.
Not that it makes much of a difference in the long run; Michael and Lincoln have been treating each other like brothers all their lives, after all. So within the fabric of the show, it won't make a great deal of difference. But I just dislike the idea of making their brotherly bond a matter of choice. I realize all too well that one can choose to disown a blood relative and embrace practical strangers as family, but it's just not as psychologically satisfying.
Christina's apparent plan (to use this incident to spark a war that will give the Company a means of funding their own Scylla-driven future programs) is a bit overly complicated, even for this series (and that's saying something). How Michael and Lincoln are supposed to overcome their current challenge and see the end of the conflict is rather hard to contemplate. At least the two of them are working together again.