Battlestar Galactica: The Plan is a nice coda to the series. It's not, as the creators would have us believe, a comprehensive overview of the story from the Cylons' point of view, nor does it explain every aspect of the eponymous plan. (For instance, there's not a word about the search for a human-Cylon hybrid.) The Plan isn't really about the Cylons collectively at all—rather, it's Cavil's story. Or, rather, it's a tale of two Cavils: one hidden in the fleet and another infiltrating a resistance group on Caprica. These two Number Ones follow very different paths following the initial Cylon attack, and they come to quite different conclusions about the morality of the war and the relationship between human beings and machines.
Cavil is (are?) a complicated character, particularly when it comes to BSG's exploration of religion. He poses as a priest, and seems to be one of the primary masterminds of what more pious Cylons consider "God's plan." But he is an atheist himself, and has no kind words for the faith of his fellow Cylons. "There is no God," one of the Cavils explains. "Supernatural divinities are the primitive's answer for why the sun goes down at night... That's what we've been telling the others for years."
His attitude toward his human progenitors—and humanity as a whole—complicates his claims of atheism. Since human beings created the Cylons (somewhere back in time, at least), human beings can be considered their gods. Cavil's diatribes against human limitations (such as the fiery anti-human sermon in the episode "No Exit") imply not atheism, but misotheism—the hatred of God. Cavil doesn't believe in the "one true God" of the other Cylons, but he does believe in, and hate, his human creators.
And that hatred of humanity is something that The Plan explores. For the fleet-based Cavil, his experience among humanity simply provides more fuel for his ire, and more opportunities for cruelty. It's his "plan" that we learn the most about-- or, rather, how his plan was spoiled at every turn, as the other undercover Cylons began to question the war and its ends. The Caprica-based Cavil begins to see nobility in the humans' fight against impossible odds. Furthermore, he realizes that human beings continue to love and care for their dead, which likely means the Final Five will also continue to love and mourn for humanity even if they are all wiped out. By the end of his story, he's begun to see the Cylon holocaust as something for which he must be forgiven, as we see in a complex confessional scene between him and Anders. "Given that this holocaust was such a journy of learning for you," Cavil wonders, "can you forgive the Cylons? Because if you can, that's really transcendent... Humanity had so much sin." But Anders is offended at the very idea of forgiving the Cylons: the Final Five will not simply forget their love for the human race once Cavil's genocidal plan is complete. Cavil seeks the approval of one of the Final Five and fails to get it—he has yet to atone for his own sins.
In addition to its rumination on the subject of human and Cylon sin, The Plan underscores something that became clear about the Cylons' religious beliefs as the series progressed: the multiplicity of their theologies. At the show's beginning, the Cylons were presented as unified in their zealous monotheism, but later episodes showed a spectrum of religious beliefs among them—from the earnest zealotry of the Sixes to Leoben's mysticism to, most tellingly, Cavil's cynical atheism. Cylon society, at first depicted as simply monotheistic, is revealed as multitheistic, as mixed and multifaceted as human society. BSG was adept at problematizing its subject matter, and the revelation of sectarian strife among the Cylons was one of the most effective ways in which the show made us question our assumptions about the badness of the "bad guys" (except Cavil, of course). The Plan is hardly the last word on Cylon religion, but it is certainly a solid exploration of the motivations of one of its chief villains.