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His closest friend among the crew is Kara Thrace. Agathon is almost always addressed by his callsign.
Before the Attack
Much of Agathon's life before the attack has not been touched, with a few exceptions. Before the decommissioning ceremony, he mentions an interest in pyramid and the fact that he has a relationship with a girl on Gemenon. Sharon "Boomer" Valerii's additional comments on this fact lend to his apparent reputation as a ladies' man (Miniseries, Night 1).
In the Beginning
At the time of the Cylon attack, Lieutenant Karl Agathon serves as ECO aboard Raptor 312 with Valerii in Galactica's last fully-operational Viper squadron, and witnesses the squadron's destruction by Cylon Raiders, after the Raiders exploit the Command Navigation Program to disable the Vipers.
Following the attack, Agathon and Valerii attempt to return to Galactica, avoiding Cylon patrols, but are unsuccessful: their Raptor is damaged in a Cylon missile strike, and Agathon receives a leg wound from shrapnel that breaches the hull. As a result of the damage received, the Raptor is forced to land on Caprica, where Valerii makes emergency repairs. Moments after Valerii's repairs, their ship is mobbed by civilians desperate to get off the planet.
With limited space for survivors aboard the Raptor, Agathon volunteers his seat to Dr. Gaius Baltar and remains on Caprica in the hope that Baltar's great intelligence will be of benefit to the Colonials in their renewed fight against the Cylons. Both Helo and Boomer feel that there is no chance that he will survive the Cylon nuclear attack on Caprica, but he chooses to stay behind anyway, sacrificing his own life so Baltar can escape the planet. Agathon is forced to shoot a desperate man clinging to the departing Raptor.
After Valerii's departure, Agathon apparently separates from the surviving refugees (who soon succumb to radiation poisoning) and flees from Cylon ground forces. After six days on Caprica, surviving on anti-radiation medication from his survival pack, he is captured by Centurions after seeing a copy of Number Six.
Agathon is "rescued" by a copy of Sharon Valerii, unaware that this is not the same one who abandoned him on Caprica. She guides him across Caprica as part of an elaborate (if potentially hastily conceived) experiment designed to make this second Valerii the object of Agathon's affections. Several situations are engineered to make this happen:
Agathon eventually admits that he has feelings for Valerii and that he would have gladly traded places with Chief Tyrol, whom he knew to be having an illicit relationship with her. Following this, the two have sex in a forest on Caprica. Afterwards, Valerii is instructed by the Five and Six overseeing the experiment to lead her lover to a nearby cabin, and to kill him if he refuses to settle there. However, the Cylon plan goes awry because Valerii has apparently fallen in love with Agathon. She forces them both on the run once more, this time genuinely seeking to escape from Caprica via the military base at Delphi, which is now under Cylon control.
During their attempts to reach Delphi, Agathon witnesses a troop of Cylon Centurions being led by Number Six - the woman he thought had been killed when Valerii rescued him. This draws him to the conclusion that the Cylons are using human clones they have created (Colonial Day). Once at Delphi, Agathon receives another shock: not only are further versions of Six on-hand - he comes face-to-face with another Valerii copy, revealing the full truth about the woman known as "Boomer" to him. Believing he was lured into a trap, Agathon goes on the run, leaving Valerii at the base.
The Valerii copy that Agathon has paired with later catches up with him, and while he shoots her in the arm, he does not kill her as she might be of use to him in escaping the planet. Caprica-Valerii then informs him that she is pregnant with his child, and that they should go to the Delphi Museum. There, Agathon is reunited with Kara Thrace (who just arrived from Galactica using a stolen Cylon Raider) immediately after she kills a copy of Number Six and retrieves the Arrow of Apollo. Thrace, realizing immediately that Valerii is a Cylon (knowing much earlier than Agathon that Cylons can mimic human form) tries to kill Valerii, but Agathon stops her because she is pregnant ("Kobol's Last Gleaming, Part II", "Scattered").
Valerii runs away out of fear of Thrace, taking her Cylon Raider. Fearing that Number Six will finish transferring her consciousness to a new body and warn the Cylons about the humans' presence in Delphi, Agathon and Thrace make their way to Thrace's old apartment ("Scattered", "Valley of Darkness"). Later, the two join up with the human resistance on Caprica (Resistance).
The Resistance and escape from Caprica
When Thrace is captured by the Cylons and taken to a "hospital", Valerii returns to aid Agathon and the resistance in rescuing her. Shortly afterward Agathon, Thrace, and Valerii leave Caprica en route to the Fleet (The Farm). The group lands on the Astral Queen, which has broken off from the rest of the Fleet. When Lee Adama grabs the new copy of Valerii and threatens to shoot her, Agathon raises his gun to Adama's head in response. They are calmed by Roslin, who then orders Valerii thrown out of an airlock. Valerii convinces Roslin of her usefulness before this happens, and later accompanies Agathon and others to Kobol to find the Tomb of Athena (Home, Part I). On the way to the tombs, Adama remarks to Thrace that he is disturbed that Agathon and this Valerii copy love each other, and Agathon admits to Valerii that he now loves and trusts her.
Home on Galactica
Agathon's welcome-home to Galactica, months after being declared missing on Caprica, isn't a generally warm one. Many in the crew find his romance with a Cylon disquieting or disgusting. A few crew warm up to him after his suggestion of using carbon composites on a newly contstructed fighter, the Blackbird, turns Tyrol's pet project into a significant asset (Flight of the Phoenix).
Chief Tyrol is still nursing the loss of Boomer (the Galactica copy of Valerii that left Helo on Caprica and later shoots Commander Adama), and now must deal with the return of another Valerii, her "memories" of him, and the fact that Agathon is romantically involved with her. The friction between Agathon and Tyrol becomes too much and a fight ensues before both realize that fighting will gain them little. The two tacitly appear to accept the awkward situation for what it is.
When Agathon and Tyrol learn of the gang-rape of the captured Cylon on Pegasus, they are shocked to learn that the "Cylon interrogator", Lieutenant Thorne, would be interrogating the incarcerated Valerii that day. Prior to this discovery, Agathon is prepared to fight the drunken Pegasus crewmembers over their disrespect, but Tyrol realizes what is coming for Valerii and convinces him to head to the brig to her aid. While they are successful in stopping the assault, Thorne is accidentally killed and the two are arrested and taken to Pegasus for trial. Admiral Cain conducts summary courts-martial on Agathon and Tyrol, finding them guilty and sentencing them to execution. When Commander Adama hears of this abrupt treatment, he launches a Raptor with Marines as well as his Viper squadrons to his men back. A standoff ensues, with not only Agathon's and Tyrol's lives in the balance, but thousands of others in the Fleet (Pegasus).
After Starbuck returns with reconnaissance images of the Cylon Resurrection Ship, Adama and Cain agree to a truce. Agathon and Tyrol are given stays of execution. While they are imprisoned aboard Pegasus, a pair of deck hands, irate about Thorne's death, assault them. Jack Fisk, the XO of Pegasus, puts a stop to this by citing regulations, but rebuffs Agathon's thanks. Like the deck crew, Fisk's life had been saved by Thorne, and he has no sympathy for Valerii, whom he views as a machine.
After the destruction of the Resurrection Ship and the death of Admiral Cain, Fisk becomes the commander of Pegasus. He returns Agathon and Tyrol to Galactica, where the former is joyfully received by Valerii.
When the dying President Roslin orders his unborn child aborted, Agathon attempts to dissuade Adama from carrying out the order in private conversation in the admiral's office, but fails. When Valerii is being brought to the medical bay for the abortion, Agathon blocks the door, his hand on his pistol. He offers to take Valerii aboard a Raptor and leave the Fleet, but is rebuffed by Adama, who tells him, "You're a soldier". Agathon retorts that he is a father, like Adama. Baltar defuses the potentially violent incident by arriving with his report on the medically useful nature of the hybrid fetus. There are no apparent consequences from his actions.
Agathon is present when his child is born. He and Valerii marvel at their baby, and Agathon shocks Valerii when he says that it almost makes one believe in the Cylon God. When Valerii attacks Dr. Cottle, accusing him of murder after he informs her of the baby's "death", Agathon tries to restrain her but ends up with Marines pointing their weapons at him as Valerii is returned to her cell.
Caprica SAR & New Caprica
Despite Valerii's continued belief that Cottle and the other humans killed Hera, Agathon is able to convince her to assist Kara Thrace's plan for the rescue of Samuel Anders and his resistance group (Lay Down Your Burdens, Part I). Agathon and the others manage to survive the Cylon assault after Cavil informs them that the Cylons have left the Colonies. With the happenstance discovery of New Caprica, the relationship between Agathon and Valerii becomes increasingly strained, due primarily to her growing depression over the loss of their child and the fact that Valerii did not inform the SAR team that Cavil is in fact a Cylon.
During the year in orbit around New Caprica, he and Sharon Valerii marry. Agathon is acting as a replacement to Felix Gaeta as Galactica's tactical officer (Lay Down Your Burdens, Part II). He is then promoted to captain and becomes the ship's executive officer. During the plans for the rescue from New Caprica, Adama finally releases Sharon, her having gained his trust and makes her an officer in the Colonial Fleet. Both Agathons are pleased by this and Sharon, later given the callsign of Athena, promises Helo that she won't betray the trust put in her. He acts as XO during the Battle of New Caprica.
After the Second Exodus
Agathon relinquishes his position as XO after the Battle of New Caprica with Colonel Tigh's return to Galactica, but Tigh's actions and attitude cause him to be relieved of duty (Collaborators). Agathon finds himself once again acting as Adama's right-hand man (Torn).
When a recently discovered virus is to be used as an agent for genocide againt the Cylons, Agathon pleads against the plan, which he sees as an atrocity. He sabotages the operation by rigging the Cylon prisoners' cells so they suffocate before they can be executed within range of a Resurrection Ship and thus download with the virus. Roslin and Adama both know the obvious culprit, but Adama, who felt the president was on shaky moral ground for using genocide as a military solution, decides not to take any action against Agathon (A Measure of Salvation).
Agathon participates in the organized shipwide fights intended to boost morale (Unfinished Business). He fights a hard match against Major Lee Adama and is declared victorious in the match after Doctor Cottle removes a battered Adama.
He returns to flight duty and pilots a Raptor during operations to replenish the Fleet's food stores (The Passage). It is during their time at the algae planet that a Cylon negotiation party aboard Galactica reveals to his wife that Hera is still alive. Though his wife initially denies the taunt, she and Agathon soon find out from Admiral Adama that it is true, much to their dismay (The Eye of Jupiter). His wife believes the only way to get their daughter back is to be resurrected inside the Cylon fleet, and begs Agathon to kill her. Being unable to dissuade her, he grants her wish. She resurrects and successfully retrieves Hera, aided by Caprica-Six (Rapture).
Although not being officially sanctioned for his earlier insubordination, Agathon is punished by being placed in charge of the hundreds of civilians which have been transferred to a refugee camp on Galactica. Among the refugees are a large number of Sagittarons, many of whom display the first symptoms of Mellorak infection. Portia King comes to Agathon and accuses the civilian physician Dr. Robert of murder after the death of her son due to the Doctor's anti-Sagittaron bigotry. Agathon begins an investigation, made difficult by several factors. Not only is Dr. Robert held in high regard by Agathon's superiors, but the claims of the Sagittarons are dismissed due to a negative view of the religious fundamentalism and ancient traditions practiced by most Sagittarons. Agathon's personal conflict with Colonel Tigh over his marriage to a Cylon is exacerbated by the colonel's prejudices to a point where Agathon hits Tigh in a crowded corridor. When he is warned by King in the middle of the night about a seriously ill Dualla (also a Sagittaron) under Robert's care, he immediately goes to Dualla's aide and finds himself in a stand-off with Dr. Robert, Dr. Cottle intervenes and reports that toxicology tests done on the deceased Sagittarons revealed no antidote but rather toxic bisphosphonate. Agathon is ordered by Tigh to arrest Robert and a short time later, Admiral Adama personally apologizes to him for not believing his initial claims about Robert and the opposition he encountered in his investigation (The Woman King). During his private meeting with Adama, Agathon confesses his role in the failed biological attack on the Cylons, but stops short of committing his testimony to paper after Adama outlines the consequences of doing so (The Woman King bonus scene).
Agathon eventually returns to flight status and is one of the second highest ranking pilots after the deaths of Kat and Starbuck (together with Showboat and Two Times). Two weeks after Starbuck's death, Agathon takes over as CAG for a visibly distraught and emotionally unstable Lee Adama who is grounded and assigned to oversee the security detail for Baltar's defense attorney, Romo Lampkin (The Son Also Rises).
After Colonel Tigh has an extreme fallback into his alcoholism at Gaius Baltar's trial, Agathon again replaces him as executive officer. He notes a feeling of apprehension, noting "something over the horizon" is coming and that it does not bode well for the Fleet (Crossroads, Part I). When Galactica jumps to the Ionian Nebula, a large Cylon force is detected closing in on them. With no means of escape the crew prepares to engage the enemy. Tigh resumes his post but Helo remains in the CIC with the command staff, noting that Viper #3 launches without a rostered pilot (Crossroads, Part II).
The return of Starbuck and after Earth
Following the apparent resurrection of his old friend, Kara Thrace, Agathon adopts a supportive but guarded attitude towards her. He recognizes her voice over the wireless, but along with many other members of the crew, Agathon looks on suspiciously as she emerges from her Viper. He encourages Thrace to continue trying to get Earth, despite the fact that no one believes her story (He That Believeth in Me). When Thrace holds President Roslin at gunpoint, Agathon asks to be allowed to talk to her, likely hoping to appeal to her on the basis of their old friendship. When Admiral Adama gives Thrace the Demetrius to try to find Earth, Agathon joins her as her executive officer (Six of One). Although he initially defends her in front of the crew despite her eccentricities and strange behavior, his loyalty comes to a breaking point when Thrace orders her crew to rendezvous with a Cylon basestar. Agathon relieves Thrace of command (The Road Less Traveled), but reaches a compromise with her, wherein he commands the Demetrius while Thrace takes a Raptor to the basestar. After 15 hours, Agathon wrestles with himself about whether to jump away or give Thrace some more time to return. Just when the crew prepares to jump, Thrace returns and the two vessels return to the Fleet together (Faith).
Agathon returns to the Fleet with the Demetrius and the rebel basestar. He travels to the basestar with Roslin and is there when it jumps away (Guess What's Coming to Dinner?). He teams up with an Eight that downloaded Athena's memories, which causes some awkwardness between them, but they come up with and to get D'Anna Biers and destroy the Resurrection Hub. When Roslin wants to double-cross the Cylons and keep Biers to herself, Agathon once again shows his idealism and argues that the humans should be honest and keep up their end of the deal. He relents when Roslin says that he is letting his relationship with a Cylon interfere with humanity's interests. During the battle for the Hub Agathon pilots a Raptor to the installation with the Eight and retrieves Biers. Once his Raptor is away from the Hub, he orders a nuclear strike on it by the Colonial Vipers which destroys the Hub (The Hub).
During the mutiny aboard Galactica following the discovery of Earth, Agathon and his family are targeted by the mutineers. In the process of seizing the Agathons, one of the mutineers, Gage, beats Helo unconscious in revenge for the murder of Lt. Thorne (The Oath). He survives this attack and is later rescued from the brig by Kara Thrace and Lee Adama.
Weeks later, Helo has a sexual encounter with Boomer, who is posing as Athena. At the time, Helo is unaware that his real wife is bound and gagged in a nearby locker. He is later horrified to discover that Boomer has not only tricked him but has also kidnapped Hera.
Helo pleads with Admiral Adama to allow him to search for his daughter, but the Admiral refuses to risk what little they have left. Eventually, Adama agrees to take Galactica and a group of volunteers on a suicide mission to rescue Hera from The Colony.
Helo is wounded in the battle to rescue Hera from The Colony. However, he survives his injuries. Helo, Athena and their daughter settle on a habitable planet which the Colonials decide to call Earth. Karl Agathon is a direct ancestor of all modern-day humans through his daughter Hera (Daybreak, Part II).
The Re-imagined Battlestar Galactica plays heavily on Greek mythology and history; the use of names such as Delphi and those of the Olympian gods is an example. Agathon's names have many possible origins