The opening scenes of The Plan occur just prior to the destruction of the Twelve Colonies in the televised miniseries, Battlestar Galactica. Humanoid Cylon John Cavil (played by Dean Stockwell) is shown leading the planning for the genocidal attack on the human race. All of the six "known" humanoid Cylons (Cavil, Leoben Conoy, D'Anna Biers, Simon, Aaron Doral, Six, and Sharon Valerii) are present in the control room of the main Cylon base. Two versions of Cavil are shown in a Resurrection Ship, with the "Final Five" Cylons in stasis in resurrection chambers. The two versions of Cavil briefly discuss their plans for "teaching a lesson" to the Final Five (who were their creators), and one version of Cavil announces his intention to witness the destruction of humanity on the ground. This version of Cavil travels to the planet Picon, where he encounters Ellen Tigh (one of the Final Five, played by Kate Vernon) in a strip club. Other characters from the series are also depicted: Gaius Baltar (James Callis) has a final meeting with Caprica Six; Samuel Anders (Michael Trucco) is shown at his Pyramid team's training camp along with the team doctor, who is Number Four/Simon (Rick Worthy); and Tory Foster (Rekha Sharma) is shown driving to an airport in an SUV-type vehicle.
The destruction of the Twelve Colonies is depicted in a series of new special effects shots, with the Cylon Hybrid seemingly narrating the destruction in a typically convoluted but poetic way. Almost all of the planets of the Twelve Colonies are depicted in short scenes. Ellen Tigh is severely wounded in the nuclear attack on Picon, and Cavil helps her leave the planet aboard a Colonial Fleet rescue ship as he feels she still hasn't learned her lesson yet and thus cannot download and regain her memories. Aboard a civilian transport, Cavil torments the half-conscious woman with descriptions of his intent to destroy humanity. Tory Foster survives the nuclear attack as well, and is wounded when her car flips over in the blast, but seems to protect her enough to survive. Anders helps console his teammates in the mountainous region where they were training. Several scenes from the television miniseries are edited into The Plan, notably shots of: Colonial One in space; Lee Adama (Jamie Bamber) helping survivors board Colonial One; Commander William Adama (Edward James Olmos) and Colonel Saul Tigh (Michael Hogan) responding to the attack on the Twelve Colonies. Another Number Four/Simon is shown to hold a job as Colonial Fleet medic, and has a wife named Giana and a stepdaughter named Jemmy.
In a scene from the end of the miniseries, Commander Adama enters his quarters to find a note informing him that there are only twelve Cylon models. A cut to Baltar implies that he left the note.
Cavil later boards the Galactica itself, where he is mistaken for a priest. Calling himself "Brother Cavil," he takes over the Galactica's chapel. The creation of Galactica's "wall of remembrance" where survivors posted pictures and mementos of their dead or missing loved ones is depicted. Using religious fliers which talk about a "plan", Cavil covertly gathers the other cylons: two Sixes, one who is Shelly Godfrey (Tricia Helfer), a Number Five (Matthew Bennett) and a Number Two (Callum Keith Rennie). Cavil tells them that he intends to continue his plan to utterly destroy the human race. He also tells them that there is a sleeper agent aboard the Galactica, a Number Eight (Grace Park), whom he also plans to use.
Back on Cylon-occupied Caprica, Sam Anders and his teammates have fled their training center for more safe quarters. They spot Cylon Centurions collecting the parts of their fallen comrades. Later, Sam and his companions, having taken up refuge in an old military compound in the mountains, launch their first attack on the Cylons, losing several people in the successful attack. Sam and Jean Barolay later observe several Number Fives burying numerous dead human bodies, realize that Cylons have taken humanoid form, and resolve to attack them. They do so later, while a Cavil version supervises the Fives' work. Cavil plays dead and survives the attack unharmed. Mistakenly believing Cavil to be a human being, Sam and his friends take the "priest" with them back to their camp while Cavil is clearly shocked to see Anders.
Back on the Galactica, the events of the first season episodes are depicted, in part. Using an elephant figurine, Brother Cavil triggers the original Cylon programming of the Number Eight known as Sharon "Boomer" Valerii. Cavil meets with Boomer to discuss ways in which she might cripple the Galactica, and Boomer comes up with a plan to bomb the ship's water storage facilities. As she tries to implement her plan, Boomer becomes increasingly distraught because she has fallen in love with Chief Galen Tyrol (Aaron Douglas). Some of the previously unknown backstory of "Water" is depicted. Cavil becomes angry when the Number Five known as Aaron Doral is exposed as a Cylon. He demands that the Number Five he has been meeting with attempt to kill Commander Adama. He does so (as depicted in the events in the episode "Litmus"). The Number Two, meanwhile, works to listen in on Colonial Fleet communications, and becomes convinced that Kara "Starbuck" Thrace (Katee Sackhoff) holds some special purpose for the humanoid Cylons. He begins to paint the nebula depicted in Season Three episodes. Cavil, realizing that the Number Two known as Leoben Conoy has had his identity compromised (as depicted in the events of the miniseries during the Galactica's re-arming trip to Ragnar Anchorage), demands that the Number Two turn himself over to the humans and attempt to deceive or kill them. He does so (as depicted in scenes from the episode "Flesh and Bone"). When Boomer's plan to deprive the Fleet of water fails (and Boomer actually helps the Galactica locate more water), Cavil demands that Boomer kill Commander Adama. She first attempts suicide, and later purposefully botches the assassination attempt. Cavil, worried about Dr. Baltar's attempt to develop a Cylon detection machine, orders the Number Six known as Shelly Godfrey to frame Baltar for treason. She does so, but her attempt fails when she purposefully turns an amateurishly manipulated series of security tapes over to Commander Adama. Her identity compromised, Cavil orders the Six into an airlock and kills her (telling her to report back to the Cylons the Fleet's location). Cally Henderson's assassination of Boomer is depicted as well. In desperation, Cavil orders the Number Four known as Simon to destroy the ship on which he lives with his family. Distraught at the idea of killing the people he loves, Simon attempts to turn his wife against him. Overcome by guilt, he reunites with her and then commits suicide by rigging an airlock to jettison himself into space, while outside of Resurrection range.
In the aftermath of Simon's suicide, there is concern that he might have been a Cylon. But his wife, Giana, reveals that he left a suicide note. Nonetheless, when Simon is revealed by Kara Thrace to be a Cylon  Giana seeks solace from Chief Tyrol—who is beginning to suspect that he himself might be a Cylon.
Meanwhile, back on Cylon-occupied Caprica, the other version of Cavil has ingratiated himself with Sam Anders. Cavil has ordered the Number Four to attempt to kill members of Sam's team, but none have died and Cavil criticizes the Four's actions. Cavil himself tries to undermine Sam's fragile psychological well-being, but Sam rejects Cavil's counsel. Starbuck returns to Caprica and meets the stranded Colonial pilot Karl "Helo" Agathon.  The two run into Anders' team, Cavil makes a failed attempt to trick Sam into thinking they are Cylons and attacking them. Helo and Starbuck join them and attack a local Cylon base. Starbuck is wounded, taken captive by the Cylons, and subjected to various breeding experiments. Anders, Helo, and the others rescue her, discovering that Simon is a Cylon in the process. Later, after Starbuck and Helo have been away from Caprica for months and return to rescue Anders' group with Galactica troops, Cavil tries to assassinate Starbuck and Anders but finds that he cannot pull the trigger of his rifle, still thinking about Anders comment that death wouldn't make him love people any less. When the Cylon Centurions attack, Cavil is forced to hide with the rest of the humans. The Centurions break off their attack. That night, Cavil sneaks from the human camp to meet with a Number Six who informs him that the Cylons have agreed to end their attacks on the human race. Cavil, who has changed his mind about humanity, agrees to pass on the message to the humans despite the Cavils voting against peace. Cavil returns to the human camp, and the humans leave the next day for the Galactica.
Meanwhile, Brother Cavil is bedeviled by the repeated appearance of a young boy named John (Alex Ferris) in his chapel. Initially, Cavil just kicks him out. But over time, Cavil appears to warm to the boy. He begins talking to him, learning the boy's name and that the boy's parents no longer want him. Cavil soon begins to feed the boy, and allows him to sleep in the chapel. One day, the boy brings Cavil the gift of an apple, and Cavil asks him if they are friends. The boy just shrugs in response. Cavil says relying on friends is dangerous and stabs him with a knife, murdering him.
The Plan ends with "Caprica Cavil" arriving aboard the Galactica, and unwittingly exposing himself and Brother Cavil as humanoid Cylons (as depicted in scenes from the second season episode "Lay Down Your Burdens"). This time it's shown that he does it on purpose to stop Brother Cavil's plans.
Brother Cavil is brought to the brig protesting that he is not a Cylon until he sees Caprica Cavil already in the brig, at which point he stops pretending. Caprica Cavil announces that the Cylons have voted to give the humans "a reprieve" because they have decided that their attempts at genocide were an error. They have left the colonies and will stop hunting the humans (this scene differs from the same scene in "Lay Down Your Burdens, Part Two": since Mary McDonnell doesn't appear in "The Plan," the Cavils's interaction with Laura Roslin, including her interrogation questions concerning what the Cylons plan to do next, is edited out, as is her order to "airlock" the two Cylons; the order is instead given first by Saul Tigh, and then reiterated by Commander Adama, neither one of whom had these lines in the original episode.)
The two Cavils argue while on their way to the airlock. Brother Cavil is in disbelief that the Cylons have decided to leave the humans alone, and continues to argue for their destruction. But Caprica Cavil asserts that Brother Cavil does not understand the nature of love. He says that the Final Five loved humanity, and that Brother Cavil is jealous of this love. Brother Cavil, he claims, does not understand that God and the Final Five will love humanity even more if the human race is extinguished.
As they are escorted to the airlock, the Cavils see all of the Final Five Cylons watching them. They admit that this wasn't the reunion they had expected. The two Cavils are then ejected into space. Beforehand, Brother Cavil reveals that there is a second Resurrection Ship nearby and they will download when they die. He plans to box Caprica Cavil and then destroy humanity once and for all, indicating that Galactica Cavil is in fact the same copy that was the main enemy throughout season four. Caprica Cavil quietly tells his other self that he knows how terrifying death can be, and offers his hand, which Brother Cavil takes. The two are ejected, and float out past the fleet. The film ends with this scene overlaid with John Cavil's fourth-season tirade lamenting his human-like body and desiring to be more like a machine so that he could "see gamma rays, hear x-rays, smell dark matter...and feel the solar wind of a super-nova" flowing over him.