Sometimes writers will wait until the end of a series to drop the most stunning of surprises into the viewer's lap, information that completely changes perception of the status quo. Often, it doesn't quite work, since those efforts are usually meant to give a struggling final season heft and meaning. Other revelations are clearly part of a larger plan, an idea that was kept close to vest until the time was right.
I'm not sure where this episode falls on the spectrum, but I do know that it left me practically clapping by the end of the episode. I love it when the villain is revealed to have a logical rationale other than the accumulation of political power. Giving the Company a reason for all the horrible things they do is a brilliant move, because it forces Michael and Lincoln to reconsider their position. What if the main fault of the Company is their determination that the ends justify the means?
Michael's epiphany is in keeping with what has been revealed about the Company in the past (almost nothing, if one thinks about it), and explains their desire for control over so much of the free world. If Scylla is the sum total of the research conducted by the Company, then its value is justified.
The implication is that the Company is fighting a war to control the initiatives that could, quite possibly, save humanity from itself. How interesting would it be to discover that the General has chosen to authorize terrible atrocities, to stain his soul beyond repair, to protect an agenda to save the world? It makes him a far more compelling villain, because he's not simply an evil, power-hungry bastard if that's true. In short, it humanizes him and the Company in one singular moment.
The other implication of the episode is that Lincoln (and later Michael) was targeted because their mother used to be part of the Company, was secretly saved by the same surgery that saved Michael, and then betrayed the Company to create a competitor. Clearly it was her voice on the other end of the broker's cell connection. Could the mother have the intention of acquiring Scylla to implement the research in the "right" way?â
Suddenly, there is a way out of the entire mess, and it's a stunning thought. What if Michael and Lincoln can only win by taking control of the very organization they've sworn to destroy? What if Michael is the perfect man to lead the Company and foster its innovations for the good of the world? With people like Lincoln, Sara, Mahone, and even Sucre behind him, Michael could change the entire landscape.
I have no idea if that's where the story is going to go; there are tons of other viable directions this could take. But even more than the hunt for Scylla itself, this plot twist has established this season as a worthy swan song to the series. This is the kind of revelation that inspires me to go back to the earlier seasons and look for the signals and signs. Could anyone have predicted that when the third season ended?