Lee Adama was born to William Adama, a veteran of the First Cylon War, and his wife, Carolanne Adama. He also had a younger brother, Zak Adama. Their father strongly encouraged both boys to enter the Colonial Fleet and become Viper pilots. Unfortunately, Zak was not a natural pilot like his brother and father, and was killed in an accident after being awarded flight status against the better judgement of his flight instructor and fiancée, then-Lieutenant Kara "Starbuck" Thrace. Zak's death drove a wedge between Lee Adama and his father that would only be healed over two years later, after the Destruction of the Twelve Colonies.
By the time of the Cylons' devastating attack on the Twelve Colonies, Lee Adama is a Captain in the Colonial Fleet Reserve with the call sign "Apollo". He is a special guest at the decommissioning ceremonies for Battlestar Galactica, commanded by his father. After Major Jackson "Ripper" Spencer, the Galactica's CAG (Commander of the Air Group) is killed in battle, Lee Adama becomes senior survived pilot, then joins the Galactica crew and becomes its CAG.
Lee Adama's strained relationship with his father also causes him to become a strong supporter of Colonial President Laura Roslin, who often butts heads with William Adama. Roslin, aware that she is unfamiliar with the military and that he can give her valuable insights in that area, appoints Lee Adama to be her personal military advisor.
Early in their relationship, President Laura Roslin often referred to Lee Adama as "Captain Apollo". Lee once corrected her, stating that "Apollo" was his call sign, but President Roslin replied "'Captain Apollo' has a nice ring to it." Upon joining Galactica's crew, Apollo was a bit of an outsider but after proving himself in several missions as more than just the "old man's son" he earned the respect of his fellow pilots and soon became one of the crew.
When Kara Thrace goes missing after being shot down over an un-named red moon, Lee is at the forefront of the search for the missing pilot. Lee and his father are ultimately compelled to abandon the search for Starbuck after President Roslin alerts them to how they are placing personal feelings above the good of the fleet. Fortunately, Starbuck is able to return to Galactica using a Cylon Raider that she shot down. However, the incident cements the father-son bond between William Adama and his surviving son. Lee questions how long his father would search for him, were he missing, to which the elder Adama responds, "If it were you, we'd never leave."
Lee is part of the strike team sent by then-Commander Adama to Colonial One to terminate Laura Roslin's presidency after she encourages Kara Thrace to abscond with a captured Cylon Raider. On board Colonial One, Lee has a change of heart, declaring that it isn't worth it to sacrifice democracy. He puts his gun to then-Colonel Saul Tigh's head. Tigh calmly tells Lee, "This is mutiny, you know that." Tigh takes control of the situation after Roslin surrenders and is able to take both Roslin and Lee into custody.
Lee is present in the Galactica's CIC shortly thereafter, when the Cylon infiltrator known as Lieutenant Junior Grade Sharon "Boomer" Valerii shoots Commander Adama twice in the chest. On Tigh's orders, Lee is physically dragged from his father's side and thrown in the brig. Needing Lee's services as CAG, Tigh later releases Lee on parole. Lee will perform his duties as before, but "make no attempt to free [Roslin] or sow insurrection among the crew", and will return to the brig when not on duty.
Nonetheless, Lee breaks his parole after Tigh's leadership takes a disastrous turn and results in civilian deaths. He helps Roslin to lead a breakaway fleet to Kobol. After Commander Adama and President Roslin make a personal effort to heal the divisions in the fleet, Lee returns to duty on Galactica. Lee is one of the five people who see firsthand the map to Earth in the Tomb of Athena on Kobol.
After the Battlestar Pegasus joins the fleet, Lee is temporarily transferred to the Pegasus, given duties flying Raptors rather than Vipers, and even demoted to Lieutenant. All of these misfortunes are reversed after the successful attack on the Cylon Resurrection ship, the death of Rear Admiral Helena Cain, and his father's promotion to flag rank. However, Lee battles with depression at this time, confessing to Kara Thrace that "he didn't want to make it back alive."
While on leave on the Cloud 9 luxury liner, Lee is accidentally shot by Kara Thrace during a hostage rescue. He takes almost a month to recover from this wound, during which time he is promoted to Major and consummates his long-simmering relationship with Petty Officer Second Class Anastasia Dualla. He is assigned to Pegasus to assist the new commanding officer, Commander Barry Garner. After he successfully commands the ship during a Cylon surprise attack in which Garner is killed, Lee is quickly promoted from Major to Commander, and given command of Pegasus.
Shortly before the Roslin-vs.-Baltar presidential election, the fleet discovers a somewhat habitable planet inside of a nebula, presumably safe from Cylon discovery, which is named New Caprica. After Gaius Baltar wins the presidential election, he orders the establishment of permanent settlements on the planet. The Galactica and Pegasus begin a monotonous orbital defence patrol.
Months later, Lee and Kara Thrace both get drunk at a party celebrating the ceremonial first shovelful of earth being dug on New Caprica. They have sex, declare their love for one another, and fall asleep together; however, Kara wakes first and leaves. When Lee wakes and returns to the settlement he finds that Kara has married Samuel Anders. This betrayal causes a lot of bad feeling between Adama and Thrace. He takes to overeating and puts on a lot of weight; he also marries his new first officer, Anastasia Dualla, now a Lieutenant Junior Grade.
Eight months later the Cylons find New Caprica, and take control over the colonists. With only a skeleton crew manning his ship, Lee is forced to flee with the rest of the fleet hoping to return again to fight off the Cylons and save the civilian population.
Four months later still, as the Galactica and Pegasus lay plans to rescue the civilians trapped on New Caprica, the psychological impact of the past year is also obvious: Lee has become more sentimental and "soft", to the point where it interferes with his ability to command the Pegasus. When contact with the resistance movement on New Caprica is established, Lee is ordered by his father to take the Pegasus and continue the search for Earth while the Galactica attempts to liberate the planet. When Galactica is near destruction, Lee and Pegasus come to the rescue, giving his father's ship time to jump out. Under heavy fire from four Cylon Basestars, the Pegasus is heavily damaged, having left its Vipers to defend the rest of the fleet. Lee orders the crew to abandon ship, saying "Thank You" to his ship just as he departs. The Pegasus rams a Cylon basestar, instantly destroying both vessels, and a large piece of wreckage damages or destroys a second basestar.
Lee's first role after the rescue of the civilian population appears to be connected to conducting some kind of head-count or census of the rescued civilians. It is in this capacity that he notices that certain confirmed survivors have gone missing, having been executed by The Circle for collaborating with the Cylons. He then returns to the role of Galactica's CAG, with the rank of Major. After much hard physical training, he loses the excess weight he gained over the previous year and asks Captain Karl "Helo" Agathon to remind him to never let himself go like that again.
Lee advocates using captured Cylons infected with a strain of lymphocytic encephalitis as biological weapons to exterminate the Cylon race. His plan is approved by President Roslin, but is thwarted by Captain Karl "Helo" Agathon, the Galactica's executive officer at the time.
The renewed strength of his bond with his father is shown when his father chooses to confess to Lee about his fears that he may have inadvertently provoked the Cylon onslaught on the Colonies.
Once the trial began, Adama is enraged that his friend and second-in-command, Saul Tigh, is exposed on the witness stand and forced to admit he killed his own wife on New Caprica. He blames Lee, believing his son has given the information to Lampkin. Adama wants Lee to stop helping Baltar, but Lee refuses, ultimately resigning his commission after Adama states openly that Lee has no integrity, and that he is "a coward" for supposedly letting Romo question Saul.
Putting the uniform behind him, Lee begins to see the trial more as a game, and personally takes up the cross-examination of President Laura Roslin, confronting her with her renewed use of the hallucinogenic compound chamala-extract, which she claims is a treatment for her relapse of cancer. This move, while justified in Lee's mind toward preserving justice in the fleet, further strains his relationship with both his father and Roslin, and motivates his wife to finally leave him.
After Laura's deposition, Lee is the last witness called, following Felix Gaeta's perjury in stating that President Baltar willingly signed a mass execution warrant. Lee proclaims in court that nearly all those in positions of power throughout the Fleet, including himself, are guilty of murder and treason to some degree; because Baltar is broadly reviled in Fleet society, human civilization is scapegoating the ex-President in an effort to expunge its guilt and shame. Lee ultimately realizes that he was being manipulated by Lampkin, who boldly predicted to Baltar that he has no greater ally than a son trying to flee his father's shadow.
After Baltar's acquittal, the Fleet is once again discovered by the Cylons. Despite having resigned his commission, Lee puts on a flight suit and pilots Viper 3 to help defend the fleet from the Cylons. While in flight he spots something on his wing, searching he discovers it to be a Viper, flown by Kara Thrace. She proceeds to tell him "It's okay, don't freak out, it's really me. I've been to Earth, I know where it is, and I'm gonna take us there".
While reviewing his gun camera footage in the pilot's ready room, Lee tells his father, who offered him his Viper wings back, that Baltar's trial may have been the catalyst, but he feels that he can do more outside the military than remaining in. Adama is visibly upset but ultimately concedes to his son's wishes.
At Lee's "mustering out" party, he drinks several toasts to the Galactica, his friends, Rear Admiral Adama, the Fleet and "to absent friends." As he leaves the Galactica, the pilots and Command staff salute him while he boards the Raptor taking him off the ship. Dualla gives him his Viper wings in a frame and as he hugs her says, "Well, looks like you get the house."
Lee begins his political career as the Caprica Delegate to the Quorum of Twelve. Following the disappearance of President Roslin aboard the defecting Cylon basestar, Lee searches for an alternative Presidential candidate to the still-divisive Zarek. After a tense confrontation with a despairing Romo Lampkin, during which he is informed of his nomination with a gun to the head, Lee accepts his candidacy. Aboard Colonial One, Lee Adama is inaugurated as the Acting President of the Twelve Colonies of Kobol.
After his father's return to Galactica, President Adama is faced with a hostage crisis instigated by the Cylon D'Anna. She demands that the Four cylons within the Colonial fleet reveal themselves and find their way to the Rebel baseship; until then, a Colonial hostage on the baseship would be killed every 15 minutes.
His father's nervous breakdown in the light of Tigh's confession gave Lee the upper hand. Within short order, he had three of the final five standing in an airlock. D'Anna was backed hopelessly into a corner and prepared to nuke the civilian fleet; the confrontation seemed hopeless until Starbuck showed up with the co-ordinates to Earth. Lee felt that withholding the information would only serve to prolong a pointless war, so shared the discovery with D'Anna. He saw to it that Cylon and Human would travel to Earth and make a new home together.
The Fleet's arrival at Earth was a bittersweet experience for Adama. Joy, elation and relief quickly turned to dismay and horror upon witnessing a devastated cityscape that was once the thirteenth colony.