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Before the Fall of the Twelve Colonies, Anders was captain of the Caprica Buccaneers. On Cylon-occupied Caprica, he becomes leader of the human resistance until they are rescued by his future wife. He later becomes aware of his true nature as one of the Cylon "Final Five" (Crossroads, Part II).
After suffering a near fatal-gunshot wound to the base of his skull during a mutiny on Galactica, he regains memories of his life as a Cylon on Earth. In the short time he has before undergoing essential surgery, he tries to tell fellow Cylons Galen Tyrol, Tory Foster and Saul Tigh their history as the Final Five, but after the surgery he is left comatose. The Rebel Cylons try to jumpstart his brain by installing a Hybrid tank on Galactica and linking him to a datastream, and though initially unresponsive he begins to act very much like a Hybrid and is able to interact with Galactica because of the Cylon repairs and upgrades throughout the ship. He dies when, as part of the Colonial plan to abandon their advanced technology and begin anew, he pilots Galactica and her fleet into the sun of the second Earth.
During his life on Earth, he also composed a song identical to the modern "All Along the Watchtower" by Bob Dylan. Dreilide Thrace and Hera Agathon independently echo this song, pointing towards their link (along with Dylan) to the same "ethereal source".
Life on Earth and The Colony
Samuel was born a Thirteenth Tribe-Cylon on Earth over 2,000 years before the Fall. He worked at a scientific research facility, and also composed a song which he played for his lover and for his fellow researchers, Saul Tigh, Ellen Tigh, Galen Tyrol, and Tory Foster. Warned of a coming holocaust by an image of a woman no one else could see, he worked with his four friends to recreate the resurrection technology used by their ancestors. When the nuclear attack on Earth came, the five of them were downloaded into new bodies on a ship in orbit.
Backtracking the path their ancestors used to find Earth, the five rediscovered the Temple of Hopes and found their way to the Twelve Colonies to warn the humans of the dangers of making robotic slaves, but arrived too late to prevent the First Cylon War because their vessel traveled at relativistic, subluminal speeds. They persuaded the Cylon Centurions enter into armistice with the humans in exchange for designing humanoid Cylon bodies and resurrection technology for their "children". They also embraced the monotheistic beliefs of the Centurions. Their first creation, Number One, turned against them, killing them by asphyxiation, boxing their consciousnesses, and later releasing them into the Twelve Colonies one by one with false memories. By having them live as humans and share their fate during the Cylon Attack, he hoped to teach them all a lesson and get them to see the truth in his views towards humanity once they died and resurrected.
The background fabricated for Anders by Number One included being born on Picon and attending Noyse Elementary School. It is unclear how many years before the Fall of the Twelve Colonies he was inserted into the Colonial population, but less than Saul or Ellen Tigh. He became a Pyramid player for the Caprica Buccaneers and was leading his team in high-altitude training in the mountains outside of Delphi when Caprica was attacked during the Cylon assault on the Colonies. The high-altitude shielded them from the blasts of the nuclear attacks and most of the radioactive fallout that followed. He and the Buccaneers become ad hoc resistance fighters from that point forward, raiding armories and collecting caches of weapons, anti-radiation medication, ammunition and supplies in the hopes of surviving and defending themselves against the Cylons. When the attack happened he said "all of this has happened before." The rest of the team (including the coach) and the survivors they found all turned to him for leadership after the attack as he seemed to have some idea of what to do. For a long time he remained unaware that he had two Cylons among his resistance force: a Simon and a Cavil who grew sympathetic to humanity through his interactions with Anders and his resistance force (The Plan).
Anders was able to rally upwards of 100 people, mostly hikers and survivalists, to his resistance against the Cylons and from the former Delphi Union High School he was able to strike back at the Cylons for nine months. Unlike Karl Agathon, the Caprica-based (and pregnant) Sharon Valerii and Kara Thrace, Anders seems to be focused more on surviving on Caprica than he is with leaving the planet.
Anders and his resistance members encounter Agathon and Thrace two months after the initial Cylon attack (Resistance). He and his men see them and Cavil (who Anders believes to be human), says that he possibly recognizes them as Cylons so Anders and his men ambush them before the situation is diffused. Anders's main focus for a time is keeping himself and his resistance movement alive long enough for Thrace to return to Caprica once again with reinforcements from Galactica and evacuate them. Before leaving, Thrace gives him her Fleet ID tags as a promise that she would come back for him. While waiting for rescue, Anders plans to locate and destroy as many Cylon hybrid-producing "farms" as possible (The Farm).
Anders and the resistance movement conduct a series of acts of terrorism against the Cylons after they appropriate Delphi for their own. His aim was to scare the Cylons into believing there is no safe place for them and to kill them in the most gruesome way possible so they remember when they are reborn what it is like to die violently, like in an explosion (Downloaded).
The most notable act of which was the destruction of a café which kill roughly 40 Cylons. After planting the bomb in a garage, Anders is trapped with the bomb after defending it from a Centurion. Hiding behind a car on the other side of the garage, Anders is mostly protected from the blast but buried under rubble. Later found by Boomer and Number Three. Anders is spared, as he would be a useful source of information. When Caprica-Six talks about genocide and God's love, Anders uses the opening to try and kill Number Three, but is stopped by Boomer. Three is more than willing to take revenge, but all are astonished when Caprica-Six kills Three. Heeding Six's orders to get out, Anders flees, still puzzled by what had transpired (Downloaded).
Rescue and Joining the Fleet
Anders survives an assault by the Cylons at the resistance's headquarters - the same morning that the Caprica SAR team lands nearby. The Cylons assaulted the remnants of the Resistance as they head for the Raptors (Lay Down Your Burdens, Part I), forcing them to go to higher ground. After the Cylons stop attacking them, Thrace (leading the rescue team) fears the worst. Anders and Thrace promise to kill each other so that the Cylons would be unable to put them in one of their farms. Miraculously, the priest of the resistance movement appears in the forest, to tell the team that the Cylons have left the Colonies.
Thrace and Anders's relationship picks up where it left off, forcing a rift to occur between Thrace and Lee Adama.
A year later, now married to Thrace on New Caprica, Anders develops pneumonia, forcing Thrace to beg Lee Adama to release some antibiotics reserved for Pegasus' pilots. After the Cylons occupy New Caprica, Anders is visited by a copy of Leoben Conoy who inquires on Kara Thrace's whereabouts (Lay Down Your Burdens, Part II). Since the Cylons had forced Pegasus and the defense fleet away from New Caprica, the antibiotics are no longer available to help Anders.
Anders recovers from his sickness and becomes a leader of the New Caprica Resistance, along with Saul Tigh and Galen Tyrol. Thrace was taken from him sometime after the occupation, and he is unsure if she is still alive (Occupation).
Four months into the occupation, contact is made with a Raptor and a rescue plan is put in motion. Anders meets Galactica's liaison officer Sharon Agathon in Breeders Canyon, and the group is ambushed by Cylon Centurions (Precipice). After the Centurions are neutralized, a map is found on a dead 'skinjob' and Anders realizes that the map is the one given to Ellen Tigh to destroy in a heating fire. Tigh is then suspected of collaborating with the Cylons.
Anders then tells Saul Tigh about his wife's betrayal. He tells Tigh that if he doesn't "take care" of the problem, someone else will. After Galactica jumps into orbit, Anders and a group of resistance fighters set off multiple bombs around New Caprica City. They then retrieve a cache of weapons hidden under the Pyramid court in order storm the detention center and free the humans imprisoned within. Inside the detention center, Anders and a team of Marines find an unconscious Kara Thrace in her apartment style prison cell. Anders begins to carry Thrace out of the center but is interrupted after Thrace regains consciousness and runs back to retrieve her daughter, Kacey Brynn. Anders finds Thrace and Kacey back at the apartment, and leads both out of the building (Exodus, Part II).
Shortly following the Fleet's abandonment of New Caprica, Anders is brought into the Circle, a secret tribunal assembled by President Tom Zarek for the purpose of judging and executing those who had collaborated with the Cylons during the occupation. Along with Chief Tyrol, he is among the more scrupulous members and soon becomes uncomfortable with the Circle's actions and leaves the group. Thrace accepts the Circle's invitation to replace Anders, an act her husband sees as a personal betrayal. He hands back Thrace's ID tag, saying he doesn't want it anymore. Thrace and Anders are still husband and wife, but the combination of Thrace's joining the Circle and her feelings for Lee Adama heavily strains their marriage. He eventually moves off Galactica to the Salpica (Unfinished Business (Extended Version)), which limits their contact to occasional visits per shuttle or participation in critical missions ("The Eye of Jupiter", "Rapture").
The death of his wife (Maelstrom) weighs heavily on Anders. Two weeks later he is found drunk on the hangar deck, standing atop of a Viper and playing with a cubit. When Lee Adama is tries to get Anders to come down, he slips, falls and breaks one of his legs. Later, Anders joins Adama at the memorial wall where Adama has put up Kara Thrace's picture (The Son Also Rises). Shortly after this, Anders decides to follow in his wife's footsteps by obtaining a commission and joining the Fleet as a pilot trainee (Crossroads, Part I), initially flying Raptors before transitioning to Vipers.
Not long after he begins a relationship with Tory Foster, he realizes that the pair of them are experiencing hearing something unusual. Later on, he discovers that Tyrol hears the strange sounds as well, but does not get the opportunity to discuss it with him. When Anders, along with Tyrol, Foster and Saul Tigh find themselves drawn to a room shortly after the Fleet arrives at the Ionian nebula, they instinctively realized that they are four of the Final Five Cylons. However, both he and Tigh agree that their lives up until that point were not in vain, and the four wordlessly agree to continue their allegiance to the Colonies (Crossroads, Part II).
He participates in the Battle of the Ionian Nebula, finding himself face to face with a Cylon Raider that he fails to destroy because his weapon safeties are enabled. The fortuitous act results in the Raider scanning Anders, whose eye flickers red. The Raider determines that he is a Cylon and as a result the Raiders abruptly abort their attack on the Fleet, forcing the whole Cylon fleet to retreat. After the battle, he recalls his experience with the Cylon Raider to the others, and wonders whether he just made a "nugget mistake" or if he was physically incapable of firing. Anders, along with the others, agree to kill themselves before they betray the humans (He That Believeth In Me).
Anders joins the Demetrius's crew on its mission to find Earth. Three weeks into the mission, he questions Thrace's command style, forcing her to open up more about her mission with her crew (The Ties That Bind). A week later they encounter a damaged Heavy Raider with a copy of Leoben Conoy aboard. Thrace allows him aboard against the crew's wishes, because she wants his help in finding Earth. When Anders sees how physically close the two are, he attacks him until Marines separate them. Later, Anders asks Conoy what he wants from Thrace. Conoy replies that he seeks to understand Thrace's unexplained destiny, which Anders doesn't consider good enough. Conoy says otherwise and that Anders might have his own destiny, beyond his relatively inconsequential life as a professional Pyramid player (The Road Less Traveled).
During the mutiny aboard the Demetrius Anders sides with Thrace, going as far as to shoot Felix Gaeta in the knee to prevent him from jumping back to Galactica. After accompanying Thrace to a disabled Cylon basestar, Anders involves himself in an execution of a Number Six model who had moments before murdered Jean Barolay. The idea of Natalie assisting to pull the trigger on another of her models disturbs him. After seeing Agathon interact with a datastream and becoming curious of what would happen if he tried it, Anders tries to connect with the datastream, but is interrupted by Kara and never gets the chance to learn what would have happened if he had succeeded. Later into the mission, however, he consoles a dying Number Eight when Sharon Agathon fails to. He then becomes visibly worried when Thrace, Natalie and Sharon deduce that the Final Five have come from and know the way back to Earth, and propose a resurrection of the Number Three model to reveal the Five's identities (Faith). Back on Galactica, Anders is distraught over the loss of Gaeta's leg, talking of how Gaeta sings all the time to cope with his pain, but can't bring himself to talk to Gaeta about it (Guess What's Coming to Dinner?).
During a confrontation with their erstwhile Cylon allies — now lead by the unboxed D'Anna Biers — interim President Lee Adama forcefully persuades Colonel Tigh to give up the identities of the other Final Five aboard Galactica, the safety of the Fleet hanging on it. Anders is arrested along with Tyrol, and they join Tigh in the launch tube airlock, under threat of being spaced in the showdown. Just as Adama is about to follow through on his threat, Thrace averts the execution with news that the three Cylons have given them the way to Earth. Anders and his fellow Cylons unexpectedly receive a full amnesty from President Adama, and are part of the landing party that finds Earth in a post-apocalyptic state (Revelations).
When Felix Gaeta and Tom Zarek enact a coup to overthrow the fleet's military and civilian leadership, Anders is abducted by his former wingman Diana Seelix and several co-conspirators and taken to the specially designed Cylon holding cell to be held as a hostage along with Caprica-Six and the Agathon family (The Oath). During a rescue attempt staged by Lee Adama and Kara Thrace, Anders suffers a bullet wound to the back of the neck and has to be carried to sickbay by Thrace and Romo Lampkin (Blood on the Scales).
The bullet entered his head, but in doing so it also unlocked previously inaccessible memories of his past. Although he suffers through a steadily worsening bout of Aphasia ("word salad"), he explains some of what he learns from his memories, elaborating on the history of the Final Five and their betrayal by their first creation, Number One, otherwise known as John Cavil. Before Anders can explain any more, he is taken to surgery to have the bullet removed so he does not suffer another seizure and die of a potential brain haemorrhage. He refuses treatment, fearing he may lose his restored memories, but Kara Thrace, still being his lawful wife, orders Dr. Cottle to remove the bullet anyway. The bullet is safely removed, but when Anders doesn't wake up as soon as expected an EEG is run on him it is discovered he has almost no brain activity (No Exit). He is visited by Ellen Tigh when she returns aboard Galactica, and when a referendum is tabled among the Final Five as to whether they should say with the fleet or strike out on their own, Saul Tigh votes "stay" on Anders' behalf, citing his ranting warning to the Five as he was being wheeled into the OR: "stay with the fleet" (Deadlock). When Thrace visits him some time later his eyes are seen to be open and there is a flurry of brainwave activity seen on the monitors around his bedside, though he does not show any signs of cognitive function just yet. An Eight by Ander's bedside surmises that his brain may simply be "rebooting," and using the downtime to repair itself. Dr. Cottle is dismissive of this idea. However, the Eight also suggest inserting Anders into the datastream to jump start his brain. (Someone to Watch Over Me).
Later, acting on the Eight's idea, the Cylons immerse him in a Hybrid pool much like those on Cylon baseships and connect him to the datastream. While connected to the stream he begins mimicking the mannerisms of the baseship Hybrids, down to the incoherent (to casual observers) but prophetic ramblings. His wife Captain Kara Thrace visits him and request to be alone with him. Saying her goodbyes she attempts to kill him by gunshot to the head. Anders in reflex action catches and almost crushes Thrace's forearm and tells her as another Basestar Hybrid had that she is the Harbinger of Death. As he does so power fluctuations, that has been going on for sometime on Galactica grow much worse, including the surging power levels of the main engines. Anders releases Thrace and the power fluctuations subside but do not end. Thrace presumably called the Cylons and Col. Tigh to assess the situation. It is determined that Anders is directly interacting with and Galactica’s power grid, inadvertently (but not the firewalled computers) via the Cylon organic resin applied to her superstructure for repair purposes. It is theoretically possible for Anders to jump the ship on his own just like a Hybrid on a baseship. Anders has effectively become the Hybrid of Galactica. Col. Tigh orders that he be disconnected. Just before he is he says "All this has happened before, and will happen again..." Removed from the datastream, Anders reverts to his comatose state. Later Kara Thrace once again visits her husband, accepting that the "old you" is never coming back, but she believes there is a pattern in the drawing by Hera Agathon that Hera gave her that turned out to be musical notes for a song Thrace's father played for her as a child. She is determined to get answers from Hybrid Anders and reconnects him to talk to him. When he is plugged back in by Kara Thrace the power surges briefly return but then subside to nothing and Samuel Anders vocalizes the line of code "New command" (Islanded in a Stream of Stars).
When he is visited again by Thrace and Admiral Adama he subconsciously flashes back to his time on Caprica as captain of the Buccaneers. He remembers an instance when he was in his team's locker room just after a game being interviewed by a sports reporter. The woman questions him on whether or not he would feel his career would be complete if he retired without ever leading the Buccaneers to a championship. Anders candidly responds by telling the reporter that in actuality, he cares little for the fame and the glamor associated with the game and more for the subtler aspects of it often missed amid the glitz. He speaks of his passion for experiencing "the perfection of creation" through his plays and movements, relating the sport to more mathematical concepts like physics; a brief moment where Samuel Anders the inventor broke through the cover of Samuel Anders the sports star. In the present, he apparently is able to give the location of The Colony to Thrace and Admiral Adama when asked although it is not shown on screen (Daybreak, Part I).
Anders is instrumental in the attack on The Colony, confusing its Hybrids at a crucial moment and disabling all the weapons. He is later present when Caprica-Six and Baltar return to the CIC with Hera and fulfil the Opera House Prophecy. After the successful return of Galactica to the new planet, Adama has him pilot the fleet and all their technology into the sun in order to have them start over. Before he dies, he briefly flashes back to his interview prior to the fall, and Kara says a tearful goodbye to him, returning to him her dog tags and telling him that she loves him. He whispers "I'll see you on the other side," paralleling Kara's final words to Lee Adama when she died. (Daybreak, Part II, Maelstrom). After all of the ships are abandoned, Anders pilots the ships into the sun, destroying Galactica and her Fleet. With the destruction of the Resurrection Hub, his death is permanent.
Attitudes toward humans
Despite his revelation to himself as a Cylon and his acceptance of it and the beating he endured during the mutiny, he seems to have remained loyal to the humans. After his discovery of his Cylon nature but before he recovered his first hand memories of his life before he was killed by Cavil and had his memories fabricated, he has displayed no hostility to them as a whole and in fact seems to be understanding of their point of view. This is characteristic of his sense of justice even when he was a Resistance fighter when he quickly accepted the Cylon Caprica Sharon, the future Athena, as genuinely fighting on the human's side. After the Exodus from New Caprica he did participate in the secret trials and executions of those thought to be collaborators but he soon lost his taste for revenge and decline to participate any longer. It is not known if he has ever uttered a statement that could be construed as anti-human. Indeed, just before beaten by mutinous crewmen that Diana Seelix had arranged to ambush him, he was apologetic for any misunderstanding of a romantic nature between them. (The Oath) Now that he has recovered his first hand memories of his previous life on Earth and since then, it is not known what would be his attitude toward the humans if he recovers from his vegetative state, but given his and the other Final Five's efforts to halt the Cylon attack on the Colonies during the first Cylon War and describing the genocidal Cavil's morality as twisted (No Exit) it seems to be favorable.