Although it doesn't answer all the questions one may have had after the series finale, such as the nature of Starbuck or the Cylon god, it does closely follow the events of the series, providing answers to questions such as how Shelly Godfrey disappeared and why Boomer didn't kill Adama when she attempted to assassinate him. It was exciting that this version of events showed the perspective of Cylons, although it was disappointing that Cavil, the one character focused on his desire to reach beyond his human limitations, was portrayed as loveless and clinging to his contempt for his surviving creators.

The Plan goes back to slightly before the attack on the Colonies. We get to see what the Final Five and Cavil were doing at the time of the attack, as well as an excellent reproduction of the Cylons' launching the nuclear holocaust on the Colonies. Cavil, ungrateful that he was brought into existence by humanity and the Final Five, seeks out Ellen and Anders to see that they learn their lesson. When Cavil finds Ellen in a bar, she states that she’s lived in this world a long time, and she’s proud to say she hasn’t learned any godsdamned lessons. Cavil wants her, Anders and the rest of the Final Five to live on and see the error of their ways. He says it’s cruel to keep them alive, but it’s necessary because even after 30 years they’ve yet to observe the moral failings of humanity.

To follow Anders, Cavil takes his guise as a priest, musing to Anders that humanity is full of sin and perhaps humanity got what it deserved, that even if the attack was not punishment from the Gods, perhaps the Cylons have taken over that role. Cavil is eager to hear Anders' confession, but when he doesn't seem repentant in the way that Cavil would like, he asks if Anders can forgive the Cylons for the holocaust, and suggests that the Cylons had their reasons for the attack, which Anders does not take well.

Back on the Galactica, we see a copy of Cavil coordinating with the Cylons in the fleet, and are provided with a more thorough explanation for many of the activities of the Cylons in the first season. As Doral has become too recognizable he is sent on a suicide mission. We see another aspect of Boomer's struggle as a sleeper agent, as even when she's aware of her identity as a Cylon her love for Chief Tyrol and Adama prevents her from carrying out her own suicide mission. We also see a Simon living in the fleet who was not in the first season. He has his own wife and family that he loves, and is unhappy about being called in to help with Cavil's plan to finish off the human species. When he is told by Cavil to blow up the ship he lives on, he ultimately decides to take his own life instead, airlocking himself outside of the range of a resurrection ship. He leaves a note for his wife, saying that love outlasts death.

Cavil doesn't seem to understand this concept, as he does not understand when Anders tells him that whether someone died wouldn't affect how much he loved them. Unfortunately, throughout the show we see few redeeming qualities of Cavil, and we do not even hear much more about how he wants to become more than his creators made him, aside from comments to Boomer that Cylons shouldn’t have to breathe. When Boomer tells him that she's happier when she believes she's human, that she actually likes herself then, he tells her to never say that, “because if that were true they win.” When the Chief comes to Cavil for counseling about nightmares he's been having that he is a Cylon, the Chief agrees with Cavil's suggestion that he's scared of trusting others, to which Cavil responds that he should be scared of trusting others because every single one lets you down.

It would seem that Cavil is intentionally made out to be evil. In his chapel in the fleet, there is a young boy we see several times who tries to sleep there. Cavil repeatedly shoos him away, though eventually he gives in and allows him to stay there. Cavil even eats an apple with him, and comments to the boy that they've become friends. After the boy shrugs in agreement, Cavil takes the knife he used to cut the apple and silently kills him, saying that “friends are dangerous things.”

If Cavil is so upset with his creators for making him what he is, then why does he cling to revenge instead of seeking to improve himself? It would have been great to see his plans to expand his senses to experience supernovas with the full electromagnetic spectrum, or to see how he engineered away his requirement for sleep. Instead, all we see are his poorly executed attempts to eliminate the remainder of humanity, or to teach the Final Five the error of their ways by making them undergo the horror of being kept alive as humans in the wake of a nuclear devastation. If Cavil doesn't like the human body and mind he's been given, then why does he keep acting like a twisted human focused on pettiness such as revenge, rather than focusing on making himself the best machine he could be?

The solution to being poorly designed by one's creators is not to teach those creators a lesson; it is to redesign oneself in a better form. Cavil could start by trying to engineer away the bitterness he has for his creators. At the very least, even a human-like mind has some capacity to rise above such things, and Cavil would have done well to use that capacity while he waited, however long it took, to develop the technology he needed to enhance his senses and improve his mind and body. With resurrection, he could have waited as long as it took. Instead, as we saw in the fourth season of Battlestar Galactica, the Cylons' entanglement with the humans not only causes suffering on both sides, but leaves Cavil without the Resurrection Hub he needs for immortality. In the end of the series, Cavil commits suicide when his attempts to regain resurrection technology fail.

The Plan ends with the events of the end of the second season, as we see two Cavils discussing their fate as they wait to be airlocked. The Cavil who was on Caprica is finally willing to admit that it was a mistake to annihilate the human race, although the Galactica Cavil promises to box him. Although it was disappointing that The Plan didn't provide a more sympathetic perspective on Cavil, we are at least treated to a fine ending for the last Battlestar Galactica movie. After we see the Cavils vented out the airlock, the camera zooms out to a brilliant display of stars and we once again hear Cavil saying:

“I don’t want to be human…I want to see gamma rays, I want to hear X-rays, and I want to smell dark matter…I want to reach out with something other than these prehensile paws and feel the solar wind of a supernova flowing over me…I’m a machine and I could know much more.”