As a 9-year-old girl on her home colony of Tauron, Helena witnessed her parents' deaths during a Cylon attack in the first Cylon War. She fled with her sister, Lucy, but the younger sibling stumbled in the rubble. Too injured to continue, Lucy pleaded for help from her older sister, but Helena froze and, seeing a Cylon landing party, ran away and hid in a nearby storage container. She was discovered there by a 0005 Centurion sentry. As it targeted her, she picked up a folding knife and prepared to defend herself. Before the Centurion could strike, however, it received orders to depart, as a treaty had been signed.
Now safe, Helena returned to where she left her sister, but the younger girl was missing. Only her doll remained. Looking into the sky, she sees a Cylon ship depart. It becomes clear that her sister has been taken for what can only be presumed is further experimentation towards creating a human cylon hybrid. In the aftermath, Helena vowed to do whatever it took to survive, hence leading her to become a "Razor".
Cain later made a name for herself as an ambitious officer in the Colonial Fleet. She was something of a rising star with strong political connections: Commander William Adama later remarks to President Laura Roslin that she was promoted "to Rear Admiral over half the Commanders on the list".
Prior to the destruction of the Twelve Colonies, Cain's flagship, the Battlestar Pegasus, was docked at the Scorpion Fleet Shipyards for a major refit. The refit team included a civilian network analyst, Gina Inviere, with whom Cain began a relationship. At the time of the attack, Admiral Cain, like many of her crew, was preparing to leave the ship on shore leave. The initial Cylon strike destroyed five Colonial vessels in Pegasus' immediate vicinity and severely damaged the Pegasus herself, killing 700 crew members. In a desperate gamble, Admiral Cain ordered a "blind jump" that took the Pegasus out of the combat zone.
In the immediate aftermath of the attack, Cain addressed her crew, promising revenge against the Cylons through a guerrilla-style war. Among her inner circle, however, she said she was not willing to foolishly risk lives in the pursuit of vengeance.
During the attack, Cain became impressed by the fortitude of her new aide, a young, impressionable officer named Kendra Shaw, and quickly took the young woman under her wing, giving her the knife she found as a child. Shaw worked with Gina to restore the Pegasus computers, and they discovered a Cylon communications relay nearby. Cain saw this as the perfect opportunity to strike back at the Cylons and ordered a surprise attack. After jumping into range of the relay, a fleet of Cylon Raiders jumped in and attacked Pegasus. Pegasus executive officer Commander Jurgen Belzen suspected that the Cylon relay was a trap and suggested a strategic retreat. Belzen's suspicions soon proved to be correct. However, Cain doubted his judgment, instead preferring to launch a full counterstrike, hoping it would catch the Cylons by surprise. This strategy did not work out at all as Cain had planned. When Belzen questioned Cain's decision and refused to carry out her foolish order to continue with the attack Cain ordered Commander Belzen to hand over his sidearm. He reluctantly handed over his pistol, and Cain shot him in the head with it. She then appointed Colonel Jack Fisk as executive officer and ordered him to launch the attack. Shocked by Belzen's execution, Fisk immediately agreed to carry out the order.
The Cylons managed to board the Pegasus during the attack, leading to the discovery of Gina as a Cylon agent. With this betrayal, heightened by her relationship with a Cylon infiltrator, Cain ordered Lt. Alastair Thorne to brutally interrogate the prisoner.
Pegasus then found 15 refugee civilian ships, but rather than protect them like Galactica did, Admiral Cain unscrupulously opted to strip these civilian vessels of any useful parts and supplies, draft any civilians who had valuable technical experience into her crew, and then leave the remaining civilians aboard their ships defenseless and at the mercy of the Cylons. If any civilians refused to join the Pegasus crew, Cain ordered that their families be executed. Overall, two families were killed under her orders until the draftees relented.
Six months after the Cylon holocaust, Pegasus was tracking a Cylon fleet when it accidentally encountered Galactica and her civilian ships. Taking over from Commander Adama as military commander of the fleet, Admiral Cain quickly arranges for Galactica's stores to be replenished from Pegasus's own, but neglects the civilian fleet, ignoring President Laura Roslin's requests on their behalf. (This would be considered a gross offense under military protocol since Roslin is acknowledged as legal authority over the military.)
Cain's chief military objective became identifying a mysterious Cylon vessel sighted in the fleet pursuing Galactica. Cain gives Dr. Gaius Baltar access to Gina to continue the interrogation and learn more about the ship, identified as a Cylon Resurrection ship. The strategic value of knocking out the Cylons' means of avoiding death is not lost on the Colonial military commanders, and so Pegasus and Galactica plan a joint operation to engage the Cylon fleet and destroy the Resurrection ship.
Concurrently with this operation, Admiral Cain and Commander Adama come into conflict over the treatment of two Galactica crew members, Lt. Karl Agathon and Chief Galen Tyrol. Admiral Cain sentences the pair to death for the accidental manslaughter of a Pegasus officer. Cain and Adama come to the brink of firing on one another's vessels before standing down and agreeing to postpone their disagreements until the Resurrection ship has been destroyed. Nonetheless, each makes plans to have the other assassinated following the successful completion of the operation. Neither plan is carried out, much to the relief of the respective assassins: Captain Kara "Starbuck" Thrace and Colonel Fisk.
Unbeknownst to Cain, Baltar also once had a relationship with a Six, and still has visions of the one influencing his decisions. As he interrogated Gina, Baltar fell in love with her. After the Resurrection Ship is destroyed, Baltar tells Gina she deserves justice and helps her escape. Gina kills her guard, steals his gun, and makes her way to Cain's ready room and shoots Cain, her captor and former lover, in the head (Cain's last words being "Frak You!"). After her death, Cain is eulogized by both Colonel Fisk and Captain Thrace, who says they are weaker without her.