In the Season III finale, "Arrival", Lili Marquette and her Jaridian husband Vorjak had returned to earth and were in a medical facility on board a freighter, waiting for Lili to give birth to her hybrid human/Jaridian child. An infusion of Taelon energy was deemed necessary if Lili and her un born child were to survive, and this had been provided by Da'an who was wheeled into the room in an unconscious state by Ronald Sandoval. Liam and Renee were searching the freighter for Lil, and there was an exchange of fire with Sandoval and agent Tate. Sandoval and Tate were wounded and escaped, leaving Liam and Renee alone with Lili, Vorjak and Da'an.

As Season IV begins, the freighter is moored somewhere in the Caribbean. Liam and Renee have been trying to contact Augur and have been unsuccessful. Liam is perplexed and says that he doesn't understand, that Augur would do anything in the world to help Lili. He wants to get Lili to a hospital and to take Da'an back to the mother ship. The auto pilot on the freighter has been set for Guadalupe. Renee says that Vorjak will resist any attempt to take Lili ashore.

Lili goes into spasms, transforming into a Jaridian before Liam and Renee's eyes, and Vorjak announces that her time has come. He activates his Sha'quarava and initiates a flow of Taelon energy between Da'an and Lili, hoping to save the life of his wife and his unborn child. Vorjak is successful and Lili's child (who simply appears on Lili's breast in a flash of light) is a healthy baby girl, but the energy drain has been disastrous for Da'an who becomes unconscious and metamorphoses into a hard blue crystalline sarcophagus shape, rather like a mummy.

Liam is shaken by what appears to be Da'an's death and says that Da'an had warned them, that he gave his life for Lili and her child. There is some discussion between Liam and Renee about the best way to transport Da'an's body without shattering the fragile crystalline shell. Liam is adamant that Da'an must be transported without disturbing his remains. Renee has been able to locate a customs officer who will smuggle everything off the ship in a banana truck. Liam continues to talk about Da'an, saying that he understood Da'an, and he could never forgive himself if anything happened to Da'an's remains in transit.

Back in Washington, Augur, dressed in a track suit and runners, is standing in a sports facility, checking his time after having a short run. A number of armed Volunteers are concealed in the bleachers and are waiting to apprehend him. Suddenly aware that he is not alone and that he is in danger, Augur places a refracting device in the middle of the field and sprints for cover, leaving behind him a confused group of Volunteers who are unable to figure out which one of the many Augurs they can see is the real one.

On the freighter, Lili is packing up her effects and preparing to leave, saying that Sandoval had thoughtfully provided everything she would need including clothes, diapers and a complete layette. She dissolves into tears and tells Liam she is glad that her brief transformation into a Jaridian only lasted for the duration of the birth. She tells Liam that she was terribly lonely during her time in space and that she missed him terribly. Renee introduces herself and says that she and Liam are working together "informally".

Liam charges Lili with selling out humanity by giving the Jaridians a working shuttle to duplicate, saying that her actions have tipped the balance in the war between the Taelons and the Jaridians. Lili says that the war is so ancient that neither the Taelons or the Jaridians remember what they are fighting about, that now the Jaridians will withdraw and let the Taelons die out. Liam intimates that Lili has been brainwashed by Vorjak. Lili is defensive and denies it, saying that she loves Vorjak, that the Jaridians are passionate noble, that they are much like humanity, and that they are unlike the Taelons in any way. She tells Liam that the Jaridians are dying, that they are burning up in their twenties, and that she and Vorjak have created a new species togther, that their newborn daughter will be the salvation of Jaridia. Lili and Vorjak have decided to name their daughter Ariel; Lili has always known that her golden child would be named Ariel.

On the mother ship, the injured Sandoval is lying on a gurney, looking up at Zo'or who demands an explanation. Sandoval says that his skrill absorbed a lethal blast during a skirmish in pursuit of the traitor Lili Marquette and the Jaridian. Zo'or berates Sandoval about not apprehending Lili (who supposedly died some months previously) and about the presence of a third living Jaridian on earth, about whom he had not been told. Sandoval blames Lili Marquette for the unpleasant situation. Zo'or threatens to perform an "involuntary mental intervention" on Sandoval to discover the truth. Sandoval promises to apprehend the Jaridian within five days and is granted a reprieve from being probed by Zo'or, who tells him that he has five days in which to correct the situation and bring him the Jaridian's head, or else it will be his head...... Sandoval looks relieved that he has been able to extricate himself from his predicament, but he also looks fearful about Zo'or's threat. As Zo'or leaves the room, Sandoval looks down at his skrill which is limp and inert.

In Washington, volunteer teams and ships are sweeping the city looking for Augur, who is being pursued everywhere he goes.

On the freighter, Lili's newborn daughter has a high temperature and Lili is distraught. Liam asks Lili why she risked having a hybrid baby and asks if she is aware that the price of her daughter's life was Da'an's life. Lili's response is defensive and hostile. The customs officer has arrived and there is only twenty minutes in which to get Lili off the freighter and to a hospital. Vorjak is angered by Liam's words and activates a portable ID dart, taking Lili and his daughter away with him to an unnamed destination.

At the Kobe Club, Sandoval is mingling with the other club members, looking suave and attired in a kimono. He enters a private room where agent Tate is being ministered to by one of the club attendants and they discuss their predicament concerning Lili and the Jaridian. Tate is cavalier about the Jaridians and suggests sacrificing them, but Sandoval tells Tate that he needs the Jaridians to destroy his enemies.

Meanwhile the FBI have been successful in tracking Lili through the portal system and have located her in Seneca Falls, New York. Sandoval and Tate agree to cover up Lili's trail and they design a story to corroborate the physical evidence.

Renee and Liam are still searching for Augur and have been unable to locate him. There is no sign of Augur's presence in his residence under St. Michael's church and his computer systems have all been shut down. Renee volunteers to shadow agent Frank Tate in an effort to locate Sandoval.

Augur who is still running from the Volunteer ships, has gone to ground in the deserted area on the edge of the city called the "fringes" and has located a friend, a young female computer hacker and cyber punk named J. Street. Augur relates his problems to "Street", convincing her to give him a new identity, to help him escape, and to contact Liam and Renee on his behalf. He is very worried about having left Liam and Renee in the lurch.

Lili, Vorjak and Ariel have concealed themselves in an storeroom at the hospital in Seneca Falls. Lili and her new born daughter Ariel are feverish, dehydrated and in distress. Lili begs a nurse to treat Ariel, but the nurse refuses to examine Ariel unless she is DNA coded. The desperate Lili wants to call Liam, but Vorjak refuses to allow it saying that no human is capable of protecting a Jaridian from the Taelons. It appears that earth's environment is slowly killing Lili, Vorjak and Ariel. The baby urgently needs another infusion of Taelon energy to lower her temperature, but that is a temporary measure and they will all have to leave the earth's atmosphere if they are to survive. Vorjak locates and steals a supply of Taelon plasma from the hospital to lower Ariel's temperature. While doing so, he wounds a security guard and is picked up on the hospital video camera. He is also seen by one of the nurses on duty.

At the Kobe Club, agent Tate contacts Sandoval to report the theft of Taelon plasma at the hospital in Seneca Falls. Sandoval travels to the hospital to interrogate the staff about the theft incident and talks to the nurse who was on duty at the time of the theft. She accesses the wounded (and unconscious) security guard's video badge and replays the video of the theft for Sandoval, who thanks her for her assistance and leaves, surreptitiously placing an attache case containing an explosive device behind a chair in the hospital waiting room. Mere moments after Sandoval's departure from the hospital, it blows up, leaving no survivors who had been witness to the theft of Taelon plasma by Vorjak.

Renee has been "tailing"agent Tate and follows him to the Kobe Club. She contacts Liam to tell him she has located Tate and suggests that he meet her at the club. When Liam arrives at the club, he meets Renee, who has disguised herself as a club attendant or geisha in a rented costume and heavy make-up. She has "borrowed" agent Tate's membership card, which she uses to gain access to the club for Liam. As Liam moves toward the booth in which Sandoval is resting, Renee stops him, asking him if he is ready to do this, saying that he could have killed Sandoval before and flinched, and that once he "crosses this bridge it changes everything". Liam says that he is ready and strides into the chamber where he confronts Sandoval at gun point, furiously accusing him of lying to the Taelons and demanding answers. Sandoval retaliates in kind, but his words are ineffective; he is obviously shaken by Liam's rage and vehemence. Liam seizes Sandoval by the throat, telling him that he is "on to him", and swears that he will return to kill him (Sandoval) if anything happens to Lili. Liam exits leaving a visibly shaken Sandoval behind him.

The next morning, in the fringes, Street awakens Augur giving him the new identity she has created for him along with a one-way diplomatic ticket to Singapore where there are no customs officials and no immigration procedures to worry about. Augur departs after asking her (again) to look after his friends.

Liam returns to Augur's place (the former Resistance headquarters under St. Michael's church) where he discovers Street. She introduces herself and plays a video in which Augur introduces her, explains his conduct and says that she (Street) will take care of them until he returns. Street notes that Liam seems to have scrambled Augur's computer system, but she is able to access Augur's computer and to track Lili Marquette to Seneca Falls, using Lili's DNA coding and pinpointing the alias which Lili had used (or been assigned by Sandoval) during her flight. Street tells Liam that the town of Seneca Falls just happens tp contain a working shuttle facility which does, in fact, contain shuttles, but is not currently in official use.

In Seneca Falls, Vorjak, Lili and Ariel have concealed themselves under a canvas tarpaulin behind the fence which surrounds the Taelon shuttle area. Vorjak is obviously very ill, as are both Lili and her daughter, Ariel. They make their way into the compound and approach the lone shuttle which is parked there just as Liam and Renee arrive. Liam asks Lili if Sandoval sent the shuttle for her, and Lili replies that she doesn't care, that they are leaving. She gets into the shuttle with Ariel, leaving behind Vorjak who looks as though he is close to death, but tells her to leave without him. Liam shouts at Lili not to engage the shuttle before he has a chance to check it out and sprints to the side of the shuttle where he examines the power core and discovers a bomb planted in it. As Lili activates the shuttle, Liam pulls out the explosive device and hurls it over the fence, where it detonates. He tells Vorjak to get into the shuttle, handing him a cartridge from the Taelon weapon he is carrying and telling him to convert it to Taelon energy and save himself. Liam then asks Lili to send him a message when she can and kisses her goodbye. The shuttle departs.

At the embassy in Washington, Da'an is lying on a dais, and Liam is looking down at his crystalline shape, musing aloud that Da'an was the best friend he knew how to be. There is a movement from the dais, and the crystalline shroud surrounding Da'an dissolves, leaving a conscious and very alive Da'an looking up at Liam. Da'an thanks Liam for his words, saying that his earlier actions had been selfless and directed toward saving Lili's baby. He tells Liam smugly that the Jaridians are not aware of the state called "crystalline hibernation", and Liam points out acidly that he didn't know about it either. Da'an continues on, saying that he knew Lili's child would require his energy to be cooled, and he tells Liam that Taelon eugenics programs have proven that cross-breeding will not repair the fundamental genetic flaw in Taelons or Jaridians. The sickened Liam says, "You used human women for your experiments?" He says that he takes back his words and that he has been fooled once again by Da'an's phony human skin.

On the mother ship, Sandoval reports to Zo'or about the destruction of the shuttle in Seneca Falls and says that Zo'or must be very relieved at the outcome of things. Zo'or says that he is thinking just the opposite and asks Sandoval about a coded message coming from deep space somewhere near the Jaridian empire. Sandoval dismisses the message as a spurious transmission.

Liam is sitting in Augur's residence with his feet up, holding a beer and gazing ruefully at the computer screen, when a message is transmitted from Lili. She, Vorjak and the baby are in good health and escaped successfully. They are close to the limits of transmission range, and they don't know when (if ever) they will be able to return to earth. She tells Liam that she loves him and ends the transmission.