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- Set during the events from the Miniseries to Season 2's "Lay Down Your Burdens, Part II," this story is told from the Cylons' perspective, centering on two distinct Cavil copies as they try to fulfill the Cylons' plan.
The story begins in medias res, with the two Cavils from "Lay Down Your Burdens, Part II" being escorted to the airlock. The two Cavils argue about the worthiness of their plan to destroy humanity, with Caprica-Cavil beginning to tell Galactica-Cavil why the genocide of humanity was a mistake.
From here, the tale begins as a single narrative, documenting the Fall of the Twelve Colonies, before splitting into two distinct but related stories on Caprica and Galactica.
Fall of the Twelve Colonies
- Two weeks before the attack, two Number Ones in a Resurrection Ship near the Colony are standing over the resurrection tanks containing insensate copies of the "Final Five:" Ellen Tigh, Saul Tigh, Samuel T. Anders, Galen Tyrol and Tory Foster. The Ones expect that the Final Five will be killed in the destruction of the Twelve Colonies and then resurrect into these bodies and apologize to the Ones for their former appreciation of humanity. One of the Ones plans on joining the active version of Ellen Tigh on Picon so that he can experience the holocaust in person, while the other One will go to Caprica to make final arrangements with their contact.
- Fourteen hours before the attack, Gaius Baltar and Six walk through the Government Center Plaza in Caprica City. Shortly after their goodbyes, Six meets up with One and passes off the access codes to the Colonial Defense Mainframe. One recommends she kill herself before the attack, suggesting poison as a relatively easy method.
- Shortly before the attack, Ellen is in the Club Pink Moon, a topless bar on Picon. The other One approaches her and strikes up a conversation, with Cavil introducing himself as a "mysterious stranger." She asks if he is a priest, and he ducks the question.
- At the Colony, the Cylon fleet stands in formation. The Hybrid gives the order and the basestars simultaneously jump to the Colonies.
- On Caprica, the Caprica Buccaneers are at a pyramid training camp in the mountains near Delphi. Among the players are Samuel Anders, Jean Barolay and Sue-Shaun. Watching from the sidelines is the team coach as well as the team doctor, a Number Four humanoid Cylon.
- In the Caprican city of Delphi, Tory Foster is driving to the airport to catch a flight to Caprica City. En route, she is talking with a man on the phone about her government work.
- Above Caprica, dozens of basestars and at least one Resurrection Ship jump into orbit. Several of the basestars rotate around their axes to form a y-pattern, allowing them to enter Caprica's atmosphere. - this has been compared to a bird folding its wings as it dives upon a prey animal.
- The Hybrid, presumably using the access codes given to Cavil by Six, infiltrates Colonial defenses.
and two other battlestars prepare to engage the Cylons above Caprica.
- On Picon, Ellen and Cavil debate the ability of people to change. Ellen's flippant, rebuking response to Cavil's argument for others needing "correcting" visibly frustrates him. She later tells him that people who let others make them change or apologize sell themselves out.
- In orbit of Caprica, three Valkyrie type battlestars led by the battlestar Yashuman, along with several wings of Viper Mk. VIIs, move to intercept the Cylons. Caprican Control reports that they are unable to track and respond to the Cylons due to a system-wide crash in the defense mainframe.
- As the Colonials prepare to engage, the Cylons use the backdoors installed by Six into the Command Navigation Program to shut down the Colonial ships. The battlestars and Vipers drift helplessly in space, unable to speak to each other.
- The Cylons launch multiple missiles towards the surface of Caprica. As they approach the ground, the missiles open up to reveal over a dozen independent nuclear warheads in each. The warheads separate, vector off in multiple directions and detonate.
- On Picon, Ellen and Cavil are startled as a nuclear shock wave hits the Pink Moon, indicating detonations on that planet as well. Cavil shields Ellen as the shock wave hits them.
- Delphi is hit, and Foster watches in horror as the shock wave consumes her vehicle.
- Anders quietly whispers to himself, "This has happened before," as his teammates react to the several mushroom clouds seen in the distance. The Four secretly smiles at the destruction.
- The Scorpion Fleet Shipyards, along with the docked Pegasus, are attacked by Cylon Raiders as multiple nuclear detonations occur across the surface of Scorpia.
- On Gemenon, Cylon forces attack a city as several ships hastily take off. On board one of them, another Four carries a young girl through the crowds of evacuating people.
- A passenger ship in orbit of Canceron is shaken by nuclear detonations on that planet. Among the passengers is a visibly happy Shelly Godfrey.
- The Hybrid reports on the successful attack on all Twelve Colonies.
- On board Galactica, Commander Adama informs Saul Tigh of the attack as the ship enters action stations.
- A wounded Foster crawls out of the remains of her car to find herself standing in the smoldering ruins of Delphi. Nearby, several SAR Raptors land, presumably evacuating Foster and any other survivors before rendezvousing with Roslin's fleet.
- Several SAR birds also comb the wreckage of Picon. In the ruins of the Pink Moon, a severely wounded Ellen has a flashback to the Fall of Earth. Cavil stands over her, assuring her that she is not going to die yet because she has more left to learn. Both Ellen and Cavil are soon evacuated by the SAR Raptors, also presumably meeting up with Roslin's fleet.
- Lee Adama helps Caprican survivors off Sharon Valerii's Raptor on board Colonial One. A distraught Giana O'Neill inquires about her husband serving in the Colonial Fleet on Gemenon.
- 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.
- Five days after the attack, the Fleet is attacked by the Cylons as they have been every 33 minutes for the past five days. On board the Rising Star, a wounded and disoriented Ellen is lying in a cramped makeshift sickbay as Cavil watches over her. Ellen does not remember who he is, but begs him to find Saul. As she passes out, Cavil says that four of the Final Five are in the Fleet; only Anders is absent.
- The ship continues to be jolted by explosions from the battle. Cavil rationalizes with himself about the necessity of keeping Ellen alive, saying that she has yet to understand her mistake in loving an immoral and imperfect humanity.
- Eight days after the attack, refugees continue to board and be processed on Galactica. Tigh remarks at the calm of the people, but Adama corrects him, saying they are just temporarily numb from the shock. As they walk through a corridor, Tigh accidentally bumps into Cavil.
- Cavil is carrying fliers, which talk about "the Plan" and encourage people to meet with him. A young boy runs by and knocks the fliers out of Cavil's hands.
- Cavil bends to pick up the fliers and is helped by a Number Six. Surprised but relieved, he hands her a flier as he notices a Simon copy going around a corner.
- He asks Socinus if he may post the fliers in Galactica's restricted area, but Socinus offers to do so for him.
- In the chapel on Galactica given to Cavil, Shelly Godfrey arrives with a flier to find the other Six, a Number Two copy and a Number Five copy assembled, all carrying fliers. Cavil notes that they are missing copies of Number Three and Four.
- Cavil reviews the original Cylon plan, which involved all the humans being killed, the Cylons downloading and the Universe "basking in justice." However, the survival of Galactica and the Fleet has prevented its success.
- Two proposes that they each work separately to sabotage the Fleet, but instead Cavil has assignments for each of them. He informs them that a sleeper agent, an Eight, is currently within the Fleet and he will speak to her.
- Cavil tasks the Two with cracking the Colonial military's technology so that they can listen into the Fleet's communications and contact any basestars in the area.
- For Shelly Godfrey, Cavil gives her the mission of sabotaging Baltar's work on the Cylon detector. As he will simply build another one if they destroy it, Godfrey is to discredit him to prevent any future work.
- As the copy of Aaron Doral aboard Colonial One was discovered to be a Cylon, Cavil tells the Five that he is too recognizable to remain in the Fleet. Instead, he gives him a suicide vest to use.
- On board the Gemenon Traveler, Leoben has successfully hacked into Galactica's military communications. He listens in as Kara Thrace and other pilots engage three Raiders. He is clearly intrigued by her.
- Cavil takes a small statue of an elephant out of his bag. As he leaves, he finds the boy that had knocked the fliers out of his hands sleeping in the chapel and kicks him out.
- In the tool room of the hangar deck, the newly enlisted Giana tells Tyrol that she needs to change out the oxygen cylinders on a Raptor. Tyrol disputes that the cylinders need changing and playfully informs her that Galactica has no replacement parts.
- Valerii enters the room looking for the Chief, where she is introduced to Giana. As she leaves, Giana quickly deduces that the two are an item.
- Back in her duty locker, Valerii finds the elephant statue that Cavil had been holding. The statue apparently unlocks Valerii's awareness of her Cylon identity, and she flashbacks to a conversation she had with Gina Inviere before becoming a sleeper agent.
- Meeting with Cavil, Valerii proposes that she sabotage Galactica's water supplies as a way to cripple the Fleet. Cavil agrees, but when he suggests that Valerii kill herself in the process, she is able to convince him that her cover is better than expected, referencing her relationship with Tyrol. Cavil laughs at the irony of her becoming romantically involved with Tyrol over all of the potential humans, then tells her to kill herself anyway.
- On the Cybele, the ship that had carried the Simon copy and young girl off Gemenon, Giana is having dinner with the two of them. Simon had previously married Giana, without revealing his Cylon identity, and adopted Giana's daughter Jemmy.
- During dinner, Cavil approaches Simon and introduces himself as Simon's childhood priest. Cavil excuses himself but asks Simon to come see him soon, giving the vague warning that he knows where Simon lives. Simon is clearly disturbed by the encounter.
- In a weapons locker, a soaking-wet Valerii informs Cavil that the charges have been placed in the water tanks. When she expresses reluctance at destroying the Fleet, Cavil rebukes and uses the statue to revert her into sleeper agent mode.
- As a panicked Valerii discusses with Tyrol what to do about the missing G-4 detonators, the charges are detonated, sending all of Galactica's water into space.
- Seventeen days after the Fall of the Colonies, the Five uses his suicide vest in an attempt to kill Adama. Only through Tigh's intervention is Adama saved.
- With Roslin's subsequent announcement that the Cylons now appear human and the distribution of pictures of both Two and Five, Leoben hides from Colonial Marines in the ducts of the Gemenon Traveler.
- Simon meets with Cavil in Galactica's chapel. While Simon proposes that he use his position as a medic to kill the humans off one by one, Cavil asks him why he won't do more.
- When Simon critiques this query by asking Cavil whether he actually has a plan, Cavil becomes frustrated by the failures of the Cylons to fully exterminate humanity. He tells Simon that they will later discuss a plan to have Simon blow up the Cybele.
- Shelly Godfrey goes to Adama and accuses Baltar of collaborating in the attack on the Colonies, using a forged photo of him placing an explosive device on the Defense Mainframe.
- Leoben continues to listen to Starbuck's exploits, painting the mandala symbolizing the Eye of Jupiter on a wall as he listens to a recording of Starbuck's engagement with Cylon Raiders above the red moon.
- Valerii finds that someone has written "CYLON" on the mirror of her locker. Meeting with Cavil while out of sleeper agent mode, Valerii suspects that she wrote the message herself. Cavil comforts her and reminds her why humanity must be destroyed. The two then share a kiss.
- Baltar confronts Godfrey in the head over her false allegations. Though she maintains her story, she seems reluctant to go through with destroying him.
- Leoben tries to convince Cavil of Starbuck's destiny, referencing her ability to fly a downed Cylon Raider without ever having done so before, but Cavil refuses to listen. Soon after, marines capture Leoben.
- Baltar is arrested for treason but saved when Felix Gaeta proves that the incriminating photos are a fake.
- As marines follow Godfrey through the corridors of Galactica, Cavil uses the other Six to make it seem as though Godfrey had suddenly disappeared.
- Cavil accuses Godfrey of failing to convincingly frame Baltar because of her love for him. She denies it, but Cavil has her kill herself by using an airlock, reminding her to give the Fleet's position to the other Cylons once she resurrects.
- Twenty-five days after the attack on the Colonies, Starbuck is interrogating the captured Leoben aboard the Gemenon Traveler. He breaks free of his constraints and pins Starbuck to a wall.
- As he holds her, he sees prophetic visions of their experiences together on New Caprica and Thrace's visions and death. The guards then restrain Leoben. Soon after, Leoben is airlocked on the orders of Roslin, with Starbuck showing him a moment of sympathy.
- Torn with grief and confusion over her identity, Valerii attempts suicide by shooting herself in the mouth.
- The young boy returns to Cavil's chapel. He tells Cavil that he is not a war orphan, but his parents don't want him anymore. Cavil tells once again tells him to leave.
- Giana returns to her quarters from work, where she and the rest of the deck crew had been analyzing the captured Cylon Raider. Simon becomes upset over how much she has been working, saying that since the Cylons are trying to kill them, they should be spending as much time together as possible. Giana is furious over his behavior and leaves with Jemmy.
- Adama asks the recovering Valerii to take a Raptor armed with nukes and destroy the basestar orbiting Kobol. Valerii, along with Margaret Edmondson, succeed in doing so and are greeted as heroes upon their return to Galactica. As Adama thanks them for their actions, Valerii pulls a gun and shoots Adama twice in the chest.
- Simon informs Cavil that Adama is dying, and that he will blow up the Cybele on the condition that his family is kept safe. However, Cavil tells him that shouldn't happen, since they will never know his true nature if they die now.
- As Adama lays in sickbay, Cavil chastises Valerii in the brig for not killing Adama. She claims that she is not fully in control of herself, but later admits her reluctance towards continuing the genocide of humanity and her attraction to her human life. Wishing her well, Cavil reactivates her sleeper agent programming and leaves. Valerii is later assassinated by Cally Henderson.
- Simon makes love to Giana and apologizes for his actions. Later, he is able to rig open an airlock on the Cybele, crying and declaring his love for his family as he is launched into space and dies permanently, outside the range of any Resurrection Ship.
- Drunk and lamenting the failures of the Cylons to destroy the Fleet, Cavil ponders the source of his bad fortunes. The remaining Six tells him the flaw in his plan: "You can't declare war on love."
- Giana is questioned by Tigh. Giana believes that Tigh thinks Simon was a Cylon, which Cavil denies. Giana shows Tigh the suicide note left by Simon, which reads, "Love outlasts death."
- Cavil finds the young boy and invites him inside, giving him food and shelter.
- Tyrol finds Giana in the corner of the hanger bay. Kara Thrace's return from her experiences with a Four copy on Caprica, along with a newspaper clipping of the Four acting as the team doctor for the Buccaneers, has proven to Giana that Simon was a Cylon. Both of them suspect that Valerii and Simon were being ordered to carry out their missions by someone else and deliberately failed.
- Giana says that were she to believe that she was a Cylon, she would climb to the top of the hangar deck and jump. Tyrol kisses her, but immediately says he didn't mean anything by it.
- After having assaulted Cally, Tyrol is being counseled by Cavil. Tyrol admits that he is afraid to place his trust in others, to which Cavil tells him he should be given his experiences.
- While reading in his quarters, Cavil is again approached by the young boy, who offers Cavil an apple. Cavil takes out a knife and cuts the apple, giving it the boy. When Cavil asks what the boy's name is, he tells him it is John.
- Cavil asks if they have become friends, and John responds that they have. Cavil tells him that "friends are dangerous things" and stabs John with the knife. He dies, and Cavil apathetically pushes his body off the bed.
- The Buccaneers panic as they listen to wireless broadcasts on the attack. Anders quickly takes charge, telling them that they have to stick together and learn more about what has happened.
- Centurions are placing their damaged and destroyed comrades in a large container. The Buccaneers sneak across a large bridge, hiding behind the railing and observing the centurions. After a Raider takes off and nearly spots them, they retreat.
- The newly-founded Resistance, made up of the Buccaneers and various hikers and survivalists, use Delphi Union High School as their headquarters.
- For their first mission, Anders uses inspiration from an old war movie, The Tauron Line. The Resistance will plant explosives on a severed Centurion thigh, wait for the Centurions to place the thigh in a recovery container and then detonate the charges.
- The Resistance quietly approaches their target and places the thigh near the container, watching from the tree line as Centurion picks up the piece. Before it goes into the container, one of the fighters slips on gravel, and the Centurion kills him immediately. Sam detonates the charge, crippling the Centurion and partially opening the container.
- Despite Anders' insistence to retreat, Kai and the coach charge towards the door with an explosives-packed pyramid ball. The damaged Centurion aims at them, and Kai passes the ball to the coach before jumping on the Centurion, which shoots and kills Kai. The coach throws the ball into the container, and the explosion knocks him off his feet, presumably wounding or killing him. As one of the teammates runs to get the coach, a Raider appears and kills him; the rest of the group retreats.
- Anders walks away from the group, arguing that he has no idea what he is doing. Barolay begs him to stay.
- Some time later, Barolay and Anders view a group of Dorals burning human bodies in a mass grave. Barolay breaks down when she notices that all of the Dorals look alike, realizing that the Cylons now look like humans.
- Anders and Barolay return with armed reinforcements as a Cavil inspects the grave. The resistance fighters kill the Dorals, and as they approach the bodies they find Cavil, pretending to be a human, calling out for help on the ground. The fighters fall for the trick, and Cavil is stunned when he sees that Anders is the leader of the Resistance.
- As they arrive back at camp, Anders asks if Cavil hears confessions. Cavil says he does, and Anders tell him they will speak later. They exit the truck, and Cavil is "introduced" to Simon, who feigns ignorance.
- One week later, Simon and Cavil speak privately. Simon asks why Cavil has yet to follow through on his plan to inform the Cylon forces of their location. Cavil sarcastically responds that Anders had asked him to hear his confession and that, as a man of the Gods, he must keep his promise to do so.
- Several weeks later, Cavil is on patrol with Anders and the Resistance when he sees Starbuck and Karl Agathon. He tells Anders that he believes he has seen them before and, thus, they must be Cylons. As the two sides engage each other, Simon calls out Cavil on his lack of effort in bringing down the Resistance.
- The next morning, Anders and Starbuck awaken together. Starbuck promises to send a rescue party for the Resistance once she returns to Galactica.
- Cavil and Simon are in the next room, where they can hear Starbuck and Anders speaking and having sex. Cavil asks why they are doing so, to which Simon responds that Anders loves her. Cavil considers Thrace to be beneath Anders and conspires with Simon to send her to the Fours' "farm" for experimentation.
- During a recon patrol, Starbuck is shot and taken to the farm. Anders returns to base with his wounded and tells Cavil the situation. Though Cavil attempts to convince Anders that Starbuck is likely dead, Anders insists on trying to find her, obviously irritating Cavil.
- The next day, Cavil joins Anders outside. Anders finally gives his confession to Cavil, where he admits his cowardice and vanity following the failed raid on the Cylon container. Cavil absolves him, then asks if Anders could forgive the Cylons considering the strength Anders have gained following the attack. Anders angrily rejects Cavil's argument and walks off.
- Simon approaches Cavil, who is upset over the fact that Anders continues to love humanity.
- At the Farm, Starbuck stabs a Four copy in the neck and escapes outside. The Resistance rescues her, and Anders orders Barolay to return to camp and kill Simon.
- Several months later, the Resistance has been heavily reduced by Cylon attacks. Anders, Cavil and the remaining survivors walk through the woods. Anders tells Cavil of his love for the people who have died under his command. Cavil angrily asks Anders why he continues to love the dead, to which Anders replies that death doesn't change love.
- Barolay tells Anders that a group of unknowns is moving towards them, and the survivors take cover. It is quickly determined that the unknowns are Starbuck, Helo and the marines Galactica has sent to rescue the Resistance.
- As Starbuck and Anders embrace, Cavil takes aim with a rifle from the distance. His gaze lingers over the backs of both their heads, but he remembers Anders' insistence that death doesn't change love and puts down the rifle.
- The Cylons begin to mortar their position, and the humans take cover. The Cylons stop firing, and both Cavil and the humans wonder why. As the humans sleep later that night, Cavil ventures out into the woods, where he finds a Six. The Six tells Cavil that the Cylons have voted for a cease-fire with the humans, and Cavil elects to deliver the message to the humans himself.
- The Resistance survivors and Thrace's team return to Galactica, where Caprica-Cavil reveals himself. The Chief identifies him as a Cylon, and Caprica-Cavil is taken into custody.
- In the brig, Galactica-Cavil enters while denying that he is a Cylon. However, his protests cease when he sees Caprica-Cavil in the cell. Caprica-Cavil delivers the cease-fire to Adama and Tigh, who decide to airlock both of them.
- 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.
- Entering the airlock, and returning to where the story began, Caprica-Cavil asks if there is a resurrection ship in range. Galactica-Cavil says that there is one but adds that he is not looking forward to dying in a vacuum first.
- Galactica-Cavil asks Caprica-Cavil whether he truly thinks that attacking the humans was a mistake. Caprica-Cavil tells him he does. Their error was that they wanted to be loved by the Final Five more than the humans, but the destruction of humanity would only strengthen the love of the Five for humanity.
- Galactica-Cavil assures Caprica-Cavil that he will have him boxed upon downloading, then resume the task of destroying the Fleet.
- As they wait in silence, Caprica-Cavil offers his hand, which Galactica-Cavil takes. They are launched into space, and as they float towards a nebula, Cavil's speech to Ellen from "No Exit" about his potential as a machine is heard.
The Universal Studios Intro for 'The Plan'
- The planet behind the Universal Studios logo at the beginning of the movie is Caprica instead of Earth.
- The Caprican landmasses shown in an orbital shot during the attack are clearly identifiable as those of Earth, specifically an inverted and stretched image of Europe, as well as Iran, the Arabian Peninsula and Turkey. This most likely represents an instance of CGI corner-cutting rather than any deeper meaning.
- One of the buildings visible in the Caprica City skyline is actually the Emirates Office Tower, located in Dubai, United Arab Emirates.
- In what is either an Easter egg (given the large amount of Battlestar Galactica filming which took place in and around Vancouver) or another CGI cost-cutting move, the MIRV is seen detonating over a large city  which is a Google Maps satellite image of downtown Vancouver, rotated by approximately 180 degrees.  The domed sports arenas General Motors Place and BC Place Stadium are clearly visible when the nuclear missiles are falling.
- The CGI landscape which appears during the Hybrid's statement that the "courthouses of Libran are burning" is the same landscape which is shown on screen as Tauron City in the Caprica episode "Know Thy Enemy". The Caprica version is widened and more buildings added. It is unclear whether the landscape in "The Plan" was intended to represent Tauron, or if this is simply another example of CGI corner-cutting by incorporating footage created for "The Plan" into Caprica.
- Unknown to the Colonials there apparently was a second Resurrection Ship nearby by the time the Cavils were executed, allowing them to download into new bodies when killed, although the Caprica copy was presumably boxed.
- Galactica Cavil was Ellen's mysterious hero that saved her from the attack on Picon. It was known to be a Number One, but it wasn't clear before this exactly which One it was.
- Whereas Scorpion Fleet Shipyards was designated as such in "Razor", the setting is identified in "The Plan" simply as Scorpia because it is meant to denote the planet as well.
- During the attack on the Colonies, after the Raiders scan the Vipers and Battestars, one of the pilots can be heard saying "I have no RADIO contact". This should be "WIRELESS" as there are no "radios" in the BSG universe.
- An outfit is listed on Propworx as being worn in the extended version of "Daybreak" by Gina Inviere, in a scene where she speaks to Sharon Valerii on a plane just before the latter becomes a sleeper agent. This is a flashback to before Valerii entered the Colonial fleet academy. This scene does not appear in the extended "Daybreak", but, as stated in Ronald Moore's commentary on that episode, it was moved to "The Plan". Thus, the Six seen speaking to Boomer in this flashback is Gina Inviere.
- The named locations on Leonis, Scorpia, Tauron, Picon, Aquaria and Libran evoke the zodiac symbols each is named for. Aerilon's association with agriculture and Caprica's association with sophisticated, urban life were established in "Dirty Hands" and "The Woman King".
- The jungles of Scorpia were also mentioned in the fourth issue of Battlestar Galactica: The Final Five.
- Reveal: When Sam and his teammates are trying to listen to a radio broadcast after the attack, and before they decide what to do, the device they are listening to is marked 'Centrios' which is an electronics brand carried by the Canadian 'Source' electronics chain before it was bought out after its parent company 'Circuit City' went bankrupt.
- Cavil puts Shelly Godfrey through an airlock weeks before Roslin "invents" airlocking as the preferred method of disposing of Cylons.
- Cavil also seems to be able to activate the airlock very quickly and without anyone noticing, whereas later in the film it took Simon a long time to rewire the airlock in order to activate it.
- Simon may have been wiring the airlock to be able to operate it from the inside, rather than requiring an external operator.
- Reveal: "Venus Eye Design V-07" can be read on the inside of the frames left behind by Shelly Godfrey. Venus Eye Design is a Canadian maker of fashion eyewear.
- Several scenes from the first two seasons of the series are shown again in this movie, but in most cases are conveniently edited to fit the story.
- Baltar's role in Boomer's suicide attempt is omitted.
- When Tyrol visits Cavil in "The Plan," Cavil asks "What's on your mind chief?" which was never asked in "Lay Down Your Burdens, Part I", and Tyrol's response in "The Plan" about how to know he is human comes much later in the actual conversation.
- Scenes on Caprica create extra moments for new dialogue to be inserted where it wasn't before. In "The Plan", a voiceover during Starbuck's rescue from the Farm has Anders ordering a resistance fighter to return to their basecamp and kill their doctor, whom they learn is a Cylon upon seeing the Simons at the farm.
- When Starbuck/Helo re-encounter the resistance on Caprica, the scene from "Lay Down Your Burdens, Part I" has the question "Is Kara Thrace there?" with Anders shouting "If she is she took her sweet time." In "The Plan", the dialogue is interrupted by Helo asking "Who wants to know?" after the question about Thrace. This scene also contains a continuity error during the switch from new footage to archive footage. As Anders and the resistance fighters are crouched behind a log, there is no one behind them in the new footage, but when it cuts to the old footage there is suddenly a soldier behind them.
- When the Cylon attack on Caprica stops, Anders asks why. In "The Plan", he is answered by Cavil with "That's a good question," a line that obviously is not in the original sequence.
- The scene of the two Cavils in the brig from "Lay Down Your Burdens, Part II" cuts most of the dialogue and rearranges it, leaving out most of Galactica Cavil's supportive statements of the new peace, and the implication he knew about the truce. Also, in the original episode, Roslin suggested throwing the pair out the airlock. Roslin does not appear at all in "The Plan" (other than a few strands of hair in archive footage of the Cavil interrogation scene), and re-dubbed dialogue has Tigh suggesting the airlock solution, with Adama agreeing.
- "The Plan" shows the end of the Cavil/Tyrol conversation from "Lay Down Your Burdens, Part I". Picking up after Cavil tells Tyrol that his deck hands are his family and taps his hands on the table, "The Plan" shows Cavil asking Tyrol if he finds it difficult to trust others. Tyrol says yes, and Cavil sympathizes with him, saying that he trusted people and they all let him down (referring to his Cylon cohorts). Cavil says it will be tough, wishes the Chief luck, and leaves.
- The iconic Cylon catchphrase "By your command" is never used in this film.
- Despite still being members of the fleet, battlestar Pegasus and Cloud Nine were not seen in any fleet shots at all, Pegasus makes an appearance briefly during the attack on Scorpia but not in the end where logically it should appear.
- The Plan also identified Rising Star as being based off the original series counterpart, confirmed Shelly Godfrey was not onboard Olympic Carrier despite claims in "Six Degrees of Separation" and saw the reappearance of Gemenon Traveller, which had only been seen in "Flesh and Bone" and on the tally boards aboard Galactica and Colonial One in "Lay Down Your Burdens, Part II".
- Cybele is first shown since making brief mentions in "Lay Down Your Burdens, Part II" and "The Passage". While the ship does bare some similarity to Scylla, seen in "Razor", it is actually a new design.
- Given the Galactica copy of Cavil's comments in the airlock, his resurrected self is the copy that led the anti-human Cylon faction during the Cylon Civil War and later killed himself permanently in CIC during the Battle of The Colony.
- It is likely that the device Leoben constructs to intercept Colonial military transmissions is a forerunner of the device he gave Laura Roslin to overcome the mutineers' communications jamming in "Blood on the Scales".
- Number One's plan to make his creators repentant is inherently flawed due to basic differences in his thinking as compared to theirs. He believes that human life is terrible and just living among humans will make them see that - a belief they simply do not share - and he does not realize the fact that inflicting suffering on the humans will make the sympathy of the five original Cylons towards humanity grow, not diminish. This holocaust mirrors that which occurred on their own homeworld and is exactly what they were trying to prevent when they made a deal with the Colonial Centurions. Number One is therefore just as naive in his expectations at the outset of the movie as are his sibling models. At the end of the movie, the One that was on Caprica with Anders has realized these errors, and the One that was on Galactica has not.
- The main focus of this movie, which is the triumph of love, shows perhaps why the Cylons eventually split into two factions. Being that it is far easier to kill people you don't know, once they start getting to know humans they are obviously having a harder time killing them. This is evident in the split during the Cylon Civil War, the three models that take the most interest in, and have the most interaction with humans are the ones advocating peace and from their interaction with humans become curious about discovering their own natures while the three models that have the least to do with humans are far more machine like and less interested in self-discovery as a result.
- The movie makes a visual point of the different evolutions of the two Cavils in one of the last scenes through intercutting, showing the murder of John by Galactica-Cavil while Caprica-Cavil considers shooting first Starbuck - which would result in her death - and then Anders - which would result in him downloading and regaining his memories but then being held prisoner while his compatriots believed him dead - before deciding to spare them.
- The characteristics of several of the Cylon models are further fleshed out.
- Number One/Cavil is clearly the leader as shown by his taking charge of the Cylons within the fleet and just like in the series this is often shown to be because his superior knowledge
- The Number Two/Leoben model is shown (as he is later in Blood on the Scales) as being very good at signal/communications cracking, this fits in well with his own obsession, and skills, with information and revelations. Two also seems to be fairly knowledgeable and Cavil seems to be slightly less derogatory towards this model, possibly because as the second model created he has known Leoben the longest.
- All the Number Four/Simon models seem to have very detailed medical expertise (enough to successfully be hired as doctors for both a pro-sports team and the military)
- Number Five/Doral is portrayed as being, as they are in other instances, very bureaucratic and obsessed with minute and unimportant details (like most bureaucrats) as well as being extremely zealous, although not particularly bright, and they seemed to be looked down upon by the other models.
- Number Six is once more portrayed as being the most varied, adaptable, and strong willed (regardless of which personality) of the Cylon models.
- Number Eight is shown being very skilled in military thinking and engineering as shown by her plan to blow the water tank but at the same time she is the most susceptible to emotions and outside influence.
- The Plan shows how Leoben knew Starbuck's name and that his belief that she had a destiny was based solely on his discovering that she learned how to fly a raider without being taught how, showing to him that she had some kind of special connection to the universe. The flashes he sees the first time he touches her, of their history together, also shows why he is so sure she will tell him she loves him and kiss him (although the flashes don't show him getting stabbed by her, hence his surprise) which also show her meeting her destiny(falling into the Maelstrom and encountering a version of him (possibly an angel) but it doesn't show anything after that, hence his surprise on seeing her dead body.
- A major plot point of "Six Degrees of Separation" was the baffling disappearance of Shelly Godfrey, seemingly into thin air. It is unclear whether or not the Colonials eventually deduced that she airlocked herself (the scene in which she is airlocked comes after the scene in which Adama is questioning her evasion of the guards).
- Tyrol's intense dreams of suicide by diving off the deck as related in "Lay Down Your Burdens, Part I," are inspired by his conversation with Giana, as depicted in "The Plan." She said that's what she would do if she suspected she were a Cylon. The chief clearly had such suspicions, and his subconscious must have latched onto her suggestion.
- The Plan does not show whether or not Boomer left the hatch combing open for Doral as Tyrol suspected in "Litmus".
- The movie exposes Ellen Tigh's explanation in "Tigh Me Up Tigh Me Down" for what she was doing during the attack on Picon as a lie. In the episode, she says she was at an airport buying a ticket to return home, presumably to be with Tigh. The Plan shows she was at a strip club getting drunk and hitting on men. It is entirely possible, however, that she was awaiting her flight.
- Before this movie, it was not clear whether Sharon Valerii carried out her actions against the human fleet (bombing the water tanks, shooting Adama) in a mindless drone state or of her own free will, albeit a will hidden from her "human" persona. The Plan establishes that the latter was the case, and that even her "Cylon side" was conflicted about her actions.
- Is the Club Pink Moon on Picon a Hat Tip to the late Nick Drake?
- Did Galactica Cavil have anything to do with the Olympic Carrier?
- What happened to the rest of the Cylon fleet; there look to be at least two dozen Basestars attacking Caprica alone, possibly more, but that many are never seen in the series and it looks like there are no more than 5 chasing the fleet after they flee from New Caprica? Are most of them still occupying the colonies? If so, then why? Are they spread out and searching other places? Where they abandoned due to lack of resources? Was the Cylon Civil war more widespread than believed?
- Did Shelly Godfrey give Galactica's coordinates to the Cylon fleet?
- Was Cavil ever linked to the murder of young John?
- If figuring out how to fly a Raider is sufficient to think a human can tap into the universal stream, is Daniel Novacek as similarly gifted as Starbuck?
- Doubtful, the Cylons let him escape in an attempt to assinate Admiral Adama so the Raider was most likely "hollowed out" before hand, which also explains why nothing is said about the Raider ever again
- Was Cavil aware Gina Inviere had joined the fleet and formed a resistance group? If so, did he order the destruction of Cloud Nine?
- Is Cavil responsible for Ellen's memory loss during her recovery on the Rising Star?
- Why does Giana not realize that Cavil must be a Cylon because a person who has never had a childhood (Simon) cannot have had a childhood priest? Did Cavil simply slip her mind?
- Why didn't the Cylons shoot down the search and rescue Raptors?
Speaking at the 2009 San Diego Comic Con, director and star of The Plan, Edward James Olmos stated that he believes there will be several more Battlestar Galactica movies in the future and is confident that the DVD release of The Plan will sell well enough to facilitate these films:
- "As a matter of fact, I've got to tell you right now. Because of you all, what you're doing, because of the love for that world...I can guarantee that this will not be the last movie." 
This statement, however, is by no means official, as both Ron Moore, David Eick, and Syfy have made no mention of any additional Battlestar films.
Olmos later went on to clarify that if The Plan sold ¾ of a million copies (750,000) then Universal Studios would assuredly be willing to produce future Battlestar-related productions.  As of November 15, 2009, The Plan had sold roughly 300,000 copies. 
- This has happened before.
- Various utterances by the Hybrid:
- Seized by God they cry for succor in the dark of the light. Mists of dreams dribble on the nascent echo and love no more. Jump.
- Counting down. All functions nominal. All functions optimal. Counting down. The center holds. The falcon hears the falconer. Infrastructure, check. Wetware, check. Everyone hang on to the lap bar, please.
- Apotheosis was the beginning before the beginning. Devices on alert. Observe the procedures of a general alert. The base and the pinnacle. The flower inside the fruit that is both its parent and its child. Decadent as ancestors. The portal in that which passes.
- Nuclear devices activated, and the machine keeps pushing time through the cogs, like paste into strings into paste again, and only the machine keeps using time to make time to make time. And when the machine stops, time is an illusion we created. Free will, twelve battles, three stars, and yet we are countless as the bodies in which we dwell, are both parent and infinite children in perfect copies. No degradation.
- The makers of the makers fall before the child. Accessing defense system: Handshake, handshake. Second level clear.
- Accepting scan. Love outlasts death.
- Their ships fail, skittering like skipped stones, and movement is meaningless in the absence of time. What never was is never again.
- The battlestar Yashuman and Caprica Control panicking as the Cylons appear over Caprica:
- Yashuman: Caprica Control, Yashuman. Heavy bogeys, six plus, lower orbit, over grid 15-2.
- Caprica Control: No joy, Yashuman.
- Yashuman: Then go to your window and look up. They’re big as frakking asteroids!
- Caprica Control: Copy, Yashuman. Still blind. Got some kind of system-wide crash in the defense grid.
- Yashuman: Try to unfrak yourself right godsdamned now, ‘cause we got multiple inbound, and they’re not carrying flowers!
- Caprica Control: Wait one, Yashuman!
- Yashuman: We don’t have one left!
- Progress reports arriving. The farms of Aerilon are burning. The beaches of Canceron are burning. The plains of Leonis are burning. The jungles of Scorpia are burning. The pastures of Tauron are burning. The harbours of Picon are burning. The cities of Caprica are burning. The oceans of Aquaria are burning. The courthouses of Libran are burning. The forests of Virgon are burning. The Colonies of Man lie trampled at our feet.
- Galactica-Cavil and Doral discussing the latter being recognizable:
- Cavil: One of your counterparts managed to get himself outed back on Ragnar Station.
- Doral: I can't understand how he was discovered. I heard it was Dr. Baltar.
- Cavil: Well, no. I'm not talking about that, exactly. I'm talking about the fact that you're walking around this fleet wearing that jacket and, more importantly, that face. You're recognizable.
- Doral: His jacket was burgundy. This is teal.
- Galactica-Cavil giving Doral a suicide vest to use on Galactica:
- They call this a 'suicide' vest, but I think that undersells all the homicide that goes along with it, don't you?
- Giana: I'm swapping out the oxygen cylinders on Raptor 702.
- Tyrol: I checked 702 yesterday. Life support's fine.
- Giana: Until two weeks ago, I used to inspect the aircraft for Sun Airways. If I found cylinders in that condition, you'd be looking at a shutdown.
- Tyrol: All right. Well, grab the spares.
- Giana: (after looking in vain for the cylinders) There are no spares.
- Tyrol: Welcome to the Galactica.
- Leoben I'm telling you. She flew a Raider. Learned how to control it from the inside. Nobody taught her how. Kara Thrace plucked that knowledge from the stream...
- Cavil I don't care if she plucked puppies from God's ass!
- Tough-Six and Galactica-Cavil drunkenly lament on the failure of the Cylons to destroy the Fleet:
- Six: You want a progress report? I'll give you a frakkin' progress report.
- Cavil: Oh, no. Please don't. Please don't.
- Six: Oh, come on, it is spectacular. Doral blew himself up, causing minor damage to a minor hallway. And Boomer jettisoned the water, and then, she personally found loads more water. (Laughing) And then she shot Adama, but not very accurately, since she loved him. And then, Leoben, he got obsessed with Kara Thrace, and then was captured and airlocked. And my sister Six utterly failed to discredit Baltar and his dreamy hair and destroyed our frakkin' cover in the process. And now Simon...Simon killed himself, really killed himself, out of resurrection range, without blowing up the ship that he lived on because he couldn't imagine life without his little human wife and his little human daughter because he loves them...
- Cavil: Stop, stop, stop.
- Six: Guess I'd better.
- Cavil: Yes. They're all letting me down.
- Six: Why are they letting you down, One? What's the x-factor? (She takes the bottle) You can't declare war on love. (She leaves)
- Cavil: I think I already did. Hey, where'd the bottle go?
- Caprica-Cavil and Simon hear Starbuck and Anders having sex:
- Cavil: What are they doing?
- Simon: You need a doctor to tell you that?
- Cavil: Oh, for God's sake, why?
- Simon: Why? He loves her.
- Cavil: He loves her?
- Simon: Vigorously.
- Cavil: But she's beneath him.
- Simon: (listening to Starbuck's moans) Not necessarily.