Caprica, 58 years before the Fall of the Twelve Colonies. Two families, the Graystones and the Adamas, are bound by a tragedy with unforeseen consequences, including the development of the Cylons.

Daniel Graystone believes his attempt to download Zoe's avatar into a cybernetic being has failed but is pleased when the soldier-cyborgs he is developing for the government finally seems to be working. He does not realize that Zoe's persona remains and is the edge that is finally making his latest invention work. Avatar Zoe is soon in touch with her close friend Lacy Rand and together they try to make sense of what has happened to her. Zoe's mother Amanda, still overwrought by their loss, attends a public memorial service for the victims of the explosion but realizing just how little she knew about her daughter, makes a startling public announcement. Joseph Adama is trying to keep his son William on the straight and narrow and desperately wants to visit his avatar daughter. In the final test of his new cyborg-soldier, Daniel Graystone wins praise from government officials for his new cybernetic life-form node, which he calls Cylons for short.

The Graystones begin to pay a heavy price for Amanda's public declaration that Zoe was a terrorist who was involved in blowing up the train. She resigns her position at the hospital and is stalked by paparazzi. The company's stock is dropping like a lead balloon and Daniel refuses to launch a publicity campaign to try and set things right. He also has to deal with Joseph Adama who insists that he find a way for him to visit with his avatar daughter. Joseph's brother Sam adds a little muscle to be persuasive. Meanwhile, Zoe's avatar has found a way to re-enter the holopad world.

Daniel Graystone gives in to the demands of his company's public relations experts and decides to go on talk show to talk about what Zoe has done and atone somewhat for any responsibility he wears for the terrorist attack. The decision to do so doesn't sit well with wife Amanda who now feels she misspoke and that they shouldn't blame Zoe for what has happened. The public appearance doesn't start well but Daniel gets help from an unexpected source. The police continue to investigate the crime and manage to get a warrant to search Zoe's and other's lockers at her school. The agent also get a warrant to search the Graystones' house but find nothing there either. Joseph Adama meanwhile pursues his revenge and sends his brother Sam to balance the score before he has second thoughts.

Tamara Adama is still trying to make sense of her "life" in her new world. She doesn't understand where she is or why she's there. She does begin to realize that she is not a pure game creation nor is she a human who has entered the game via a holoband. Or at least not a conscious human, which is one of the suggestions put to her to explain how she fits in. She's become friendly with a young man who spends most of his life in the cyberworld preferring it to "real" life. She asks him to contact her father. Joseph Adama meanwhile realizes that unless he can put his wife and Tamara's death behind him, his son William will take a path in life that will no doubt lead to a life of crime.

Daniel Graystone's longtime rival Tomas Vergis, a Tauron, reappears on the scene. Vergis accuses Daniel of stealing the MCP chip technology from him, something Daniel denies. He visits Joseph Adama to find out how Vergis got his information. Sister Clarice visits Amanda Graystone, with interesting results. Joseph Adama meanwhile buys himself a holoband, intent on finding Tamara. He also tracks down the young man who told him of Tamara's existence.

Amanda Graystone continues to struggle with all of the events in her life and now thinks she' seen her dead brother Darius. Sister Clarice befriends her convinced that determining Zoe's present state will give her the understanding of life ever after. Knowing that Sister Clarice is looking for her and may interfere with her leaving Caprica, Zoe pushes Lacey to finalize arrangements for their departure while trying to arrange for her own escape, in Cylon form, from her father's lab. Lacey has run into problems however. Joseph Adama has tracked down Tad Thorean and gets him to show where Tamara's avatar is to be found. Tad tries to explain to him that she isn't real but Joseph doesn't quite see it that way. In New Cap City, Joseph continues to learn the rules but is soon on his own. Daniel Graystone continues to spar with rival Tomas Vergis.

In New Cap City, Joseph Adama continues to follow Emmanuelle who introduces him to a drug - essentially a hack - to keep him in the game. He has trouble with the violence he finds there but his brother Sam has a suggestion for him. Daniel Graystone is now convinced that Zoe's avatar hasn't been lost but is inside the Cylon. He thinks he has a way to get to her but she's one step ahead of him. Amanda Graystone continues to see her dead brother and has flashbacks to the night he died. Tomas Vergis tells her about Daniel's theft of the MCP.

With his company's stock falling in price and unable to meet the contract to provide 100,000 Cylon robots in a month, Daniel Graystone has no choice but to sell his sports team to Tomas Vergis. With only a week to deliver the duplicated MCPs, he also decides to wipe the chip clean and mass produce a blank copy. Daniel's decision forces Zoe to reveal herself. Sister Clarice decides to face Barnabas and the internal challenge to her leadership of the STO head on. Barnabas isn't going to take it lying down and he comes through for Lacy but he expects her to perform a task for him. Amanda's mental condition continues to deteriorate. Sam is concerned about Joseph's apparent addiction to the v-world. Emmanuelle confronts Tamara in an effort to get her to help her father and her solution is quite drastic.

Daniel is grieving the loss of his company, his daughter and his wife. Vergis has taken over Graystone Industries and is mass producing Cylon Centurians. Daniel goes to Joseph and the Guatrau for help against Vergis. Zoe enters New Cap City. Clarice is visiting the STO on Gemenon and runs into problems trying to convince them to follow her vision of apotheosis. And she has a traveling companion.

Sister Clarice ruthlessly wields her new power as head of the Caprican STO as she aims to finish her war with Barnabas once and for all. Agent Duram helps Amanda make an alarming discovery.

Zoe's search for Tamara within the cruel V-World comes to an end as Zoe is shocked to see what Tamara has become. Lacy struggles to keep Zoe's secrets amidst Clarice's physical and psychological torture. The conflict between Daniel and Vergis comes to a violent head.

Sam Adama's illegal gun trade puts his life in danger, as he turns to an unlikely ally for assistance. Daniel's involvement with the Ha'La'Tha deepens.

Lacy's journey to Gemenon turns into a life or death race against the clock. The pressure on Amanda and Duram for evidence mounts as Clarice gets one step closer to Apotheosis.

Joseph and Sam Adama revisit their past on Tauron and must make a decision about where their loyalties lie. Daniel discovers Zoe's avatar has survived, while Duram is burned at the GDD.

The Graystones search New Cap City for Zoe, while Lacy uncovers a mystery about the Cylons. Clarice learns the truth about Amanda.

The Graystones find Zoe with a vengeful Clarice closing in, while the Ha'La'Tha turns on the Adama brothers.

Daniel, Amanda, and Zoe race to stop Clarice's master plan and save thousands of lives before Caprica is changed forever.