In the final episode of the first season, "The Joining", Companion agent Siobhan Beckett was unconscious and had been brought by Lili Marquette to the infirmary at Resistance Headquarters beneath St. Michael's Church. She was examined there by Dr. Parks who discovered that Siobhan was pregnant as a result of her joining with the last of the Kimera, Ha'gel, who had assumed the physical persona of Ronald Sandoval. Dr. Parks spoke of this development as the fulfilment of "Ha'gel's master plan".

Only nine hours after the joining, Siobhan goes into labour. Jonathan Doors is fearful, and at his instructions, Lili evacuates headquarters of all personnel except Siobhan, Dr. Parks, Doors, Augur and herself. As she escorting personnel from headquarters, Lili notices that Rayna is acting strangely and asks one of the Resistance members to keep an eye on her. Doors is certain that, given the unusual circumstances of its conception and birth, Siobhan's child cannot possibly be human.

During labour, Siobhan's CVI breaks down, and Dr. Parks believes it is due to its overloading during the joining with Ha'gel. Siobhan's labour is a difficult one, but Dr. Parks refuses to give her anything for her pain because it may hurt the baby. Siobhan refuses to take anything, saying she will be all right, and that the child must not be endangered. Lili promises that no one will hurt the child, and Siobhan tells Lili that Ha'gel showed her everything during the joining.

Rayna walks away from St. Michael's; when a Resistance member who asks her where she is going, she attacks him.

Inside Resistance Headquarters, the moment of birth arrives, and there is considerable anxiety. Augur compares the situation to "Rosemary's Baby", but the child, when it is born, appears to be a healthy male of typical human appearance. Siobhan names her son Liam and extracts promises from Lili and Augur to take care of Liam no matter what happens. Doors is also present, but he does not promise to protect Liam. He is frightened by Siobhan's words "no matter what happens". Within moments of his birth, Liam develops from a newborn enfant into a toddler and tells those present that his name is Liam. It is obvious from the beginning that this is a child with an astonishing intellect and other extraordinary gifts, constructing complex origami figures and assembling a Taelon puzzle toy which even Augur was unable to put together.

Dr. Parks and Doors discuss the child, Liam. Doors is curious about whether or not Liam's first words, which were a complete sentence were a fluke, as he has said nothing more. Dr. Parks does not believe so; Da'an has told her that all Taelons are born with the complete genetic knowledge of their parents. Doors speculates that if Liam's race are like the Taelons, then Liam knows everything known by his three parents, Siobhan, Sandoval and Ha'gel.. Dr. Parks has performed an analysis of Liam's DNA and points out the loose stand running through the middle and forming a triple helix rather than the double helix which is characteristic of humanity. She tells Doors that Liam is two thirds human. Doors is worried because they have no idea what Liam is capable of. He is the first of his kind. At this moment Liam undergoes another burst of physical development and becomes a young man.

Lili is summoned to a meeting with Sandoval in Boone's office.

Rayna enters the Pentagon's communications centre in Alexandria, Virginia, where she assaults a guard to gain access.

Sandoval informs Lili that Commander Boone has died of his injuries. This is a lie since Sandoval was present when Zo'or killed the unconscious Boone. Sandoval tells Lili that Siobhan was convinced she was a Resistance spy, but that he did not believe her accusations for a moment. He is impressed with Lili's performance and promotes her; she will report directly to Sandoval.

At the Pentagon communications centre, Rayna assaults a technician in the lab after asking him whether the Taelons are still blocking communications with deep space.

Da'an enters the chamber in which Boone was being treated in a liquid regeneration chamber (blue tank) and uses his psychic ability to determine the exact manner of Boone's death. When Zo'or enters, Da'an tells him that he (Zo'or) should have been aware of the psychic link between Boone and himself. Zo'or claims that it was a mercy killing., and when Da'an asks Zo'or where murder fits in the lexicon of mercy, Zo'or replies that it does "when what is gained outweighs that which is lost". Zo'or suggests that Da'an is not without stain as he issued the instructions which led Sandoval to kill Boone's wife, Caitlin. (Season I, "Truth")

At Resistance Headquarters, Doors and Dr. Parks are trying to decide what to do with Siobhan Beckett following the birth of her son. There are three options, kill her, keep her captive forever, or return her to the Taelons, which is not an option since she has now seen the Resistance Headquarters. Dr. Parks suggests a fourth option, that she repair and reprogram Siobhan's CVI, removing all memories of the joining, the birth of Siobhan's son, and her sojourn at Resistance Headquarters. At the same time, she will program the CVI to self-destruct and kill Siobhan if those memories ever resurface. Doors tells Dr. Parks to proceed. He is afraid of Liam and Liam's probable links with the Commonality and bribes Augur with a piece of modern art to remove Liam from the Resistance Headquarters.

At the Pentagon communications centre, Rayna transmits a radio signal which passes through the Taelon blockade into deep space. After doing so she transforms herself into a replicant, fires on the security team sent to apprehend her, becomes invisible and disappears.

Rayna's transmission has been detected by the Taelons who identify it as being similar to the signal emitted by a probe discovered in Russia and destroyed some time previously. Humanity do not know of the existence of the first probe as the Taelons had requested that it be kept secret. There is some discussion among the Synod leader, Qo'on, Da'an and Zo'or about whether humanity should be informed about the probe. Qo'on is against informing humanity. Zo'or feels that humanity must be told and that such an opportunity must be embraced; Da'an also feels that humanity should be told, but for different reasons, in order to prepare them for the coming Jaridian invasion. Zo'or's final words are that our "survival is all that matters".

Augur takes Liam back to his place of residence where he receives a call from the tearful Lili telling him about Boone's death, the funeral arrangements and her promotion. Liam's ability to access the Commonality becomes apparent when he has a flash back of Boone's death and tells Augur that Boone was killed by a Taelon, not his father, Ha'gel. Liam insists on learning everything about Boone and with the assistance of Augur, assimilates all the available information on Boone in Augur's computer system at breathtaking speed.

Lili informs Doors about Boone's death; Doors is completely unmoved by the news and tells Lili that he will have to be replaced. Lili tells Doors she has been promoted and sarcastically offers to replace Boone within the Resistance.

Qo'on, Da'an and Zo'or attend Boone's funeral service; Sandoval, Lili and a military guard of honour are also present. Sandoval delivers the eulogy, almost breaking down once or twice during his delivery. During the eulogy he quotes the Shao-lin monk Li Chang as saying "It is a rare occasion to be born a human being". Sandoval goes on to say: "If this is so, then William Boone is one of the rarest of the rare. For he died true to the spirit with which he lived: a sword in one hand, and an olive branch in the other. We will miss him." As he states the last words of the eulogy, he looks directly at Zo'or:

"The laurel is green for a season; love is sweet for a day. But love grows bitter with treason, and laurel outlives not May."

Liam arrives unexpectedly on the scene dressed as a major in the U.S. Rangers. Lili begins to reprimand him and he motions her to silence. The Jaridian replicant suddenly materializes in the cemetery and Liam is able to sense its presence although it is invisible to everyone else. He has a sudden premonition of impending death and pulls Da'an to safety on the ground, but the replicant fires, killing the leader of the Synod, Qo'on. Sandoval fires on the replicant with his skrill, stunning it. As Liam reaches down to assist Da'an in getting to his feet, their hands touch and something passes between them. Da'an, who is psychic, realizes that this is no ordinary mortal. Liam introduces himself to Da'an as Major Liam Kincaid who served with Boone in the SI wars.

At Resistance Headquarters, Doors and Lili reprimand Liam for appearing at Boone's funeral in uniform and Augur confesses that he assisted Liam in concocting his cover. Doors is of the opinion that Liam doesn't know what he is doing and cannot be trusted. Liam who is less than a day old, rather brashly tells Doors that he might want to reserve judgment in the matter. As the discussion is ending, Lili receives a message from Sandoval telling her to locate Major Liam Kincaid and that Da'an wishes to see Liam on the mother ship immediately.

As Liam arrives at the mother ship, Joshua Door is leaving. He has arranged a meeting with the Taelons to learn the truth about Qo'on's'death and the replicant. Zo'or and Sandoval tell Joshua about the replicant, the Jaridians and the impending invasion of Earth.

After Boone's funeral and the death of Qo'on the Taelons have retreated to the mother ship for safety and Da'an has agreed to return to Earth only to lure the replicant into the embassy so it can be destroyed. His sole condition for doing so is that Major Liam Kincaid be appointed his new protector. During his interview for the position, Liam speaks of the runes, specifically Sowelo, the Irish rune of inevitability and says that the fates of humanity and the Taelons are intrinsically linked. This knowledge was inherited from Sandoval who is, after all, one of Liam's two fathers. Sandoval who remembers Siobhan's reverence for the runes, is shaken by Liam's reference to the runes. He asks Liam if he is willing to be implanted with a CVI and Liam's stony silence is proof of his reluctance. Zo'or solves the impasse by decreeing that a CVI will not be necessary. After the interview, when Sandoval queries Zo'or about allowing Liam to proceed without an implant, Zo'or tells him that it will better serve their interests if Liam is not implanted. Zo'or wishes to become the new leader of the Synod with no resistance from Da'an. The easiest way for him to succeed will be if Da'an is killed by the replicant and that will be easier if Da'an's protector does not possesses a CVI or a skrill.

The trap to snare the replicant in the embassy is set. Liam is given a specially engineered weapon by Sandoval, which is actually ineffective and therefore useless. Liam and Da'an are told to remain close to the ID portals in Da'an's office are their only egress if things go wrong. Sandoval and Lili position themselves across the street from the embassy with monitoring equipment. As they wait for the replicant to walk into the trap, Da'an and Liam play a Taelon game called Lasha. It is the first time Liam has ever played, but he easily defeats Da'an, who with a few words cleverly disguised as a reference to the game, lets Liam know that he is aware that Liam is not what he seems to be.

The replicant materializes in the embassy and destroys the ID portal, cutting off Liam and Da'an's only avenue of escape. Liam and Da'an flee through the embassy's tunnels followed by the replicant and find themselves at a dead end. Liam fires on the replicant with the weapon given him by Sandoval., discovers it is useless and attacks the replicant with a long handled implement laying nearby. The replicant retaliates by firing a blast of energy at Liam and hurling him against a wall. As the replicant prepares to fire a second time, Liam throws up his hands in front of his face to defend himself and his palms begin to glow. He has inherited the gift of the Sha'karava from his alien father Ha'gel and possesses the ability to hurl bolts of energy from his palms. The replicant is blown apart by the blast of energy fired by Liam, who is stunned to discover he possesses such an ability. Sandoval and Lili appear on the scene moments later to find shards from the replicant scattered everywhere in the tunnel and the useless weapon lying on the tunnel floor. Sandoval comments that the weapon proved effective, and Liam retorts that it was just as effective as Sandoval meant it to be.

Siobhan Beckett is discovered wandering through the streets of the city, confused and disoriented, and is brought to Sandoval, who is surprised and happy to see her, as Lili had told him she was dead. He rather gently asks her what she remembers, but she can remember nothing between the moment she began searching for Ha'gel and the time she awoke in an alley. She is in great pain. Liam enters the office and Siobhan instinctively recognizes her son, although she does not consciously remember meeting him; blood begins to flow from her ear. Liam introduces himself to her as Da'an's new protector and denies ever having met her, although it is painfully obvious that he wishes to make contact with his mother