The American Companion Da'an is due to arrive in a Midwestern city on an official visit and Police Captain William Boone has been prevented by the Companions from implementing all the security arrangements he requested. The alien leader arrives in a Taelon shuttle from Washington, chauffeured by Marine pilot Captain Lili Marquette. Da'an has a special announcement to make about a new venture with one of the Earth's biggest industrialists, the eccentric billionaire Jonathan Doors. The Taelon front man, FBI Agent Ronald Sandoval, discounts Boone's apprehensions about controlling the huge crowd and securing neighbouring buildings so when Da'an arrives, Boone enlists the help of Lieutenant Bob Morovsky. Despite their precautions, a shot is fired from a nearby building. Doors takes the bullet meant for Da'an. Sandoval uses his Scrill (a weapon), to dissolve the building wall, revealing a lone gunman, Eddie Jorda
Da'al is kidnaped by Major MacIntire at a conference of eminent astronomers. Commander Boone queries the resistance and must find the soldiers who took Da'an and save him even if the soldiers, who are also anti-Taelon, must be killed.
Just Nine hours since Beckett conceived, The child is born and reaches maturity within minutes. Sandoval reveals Boone's ultimate fate to Lili. And The Resistance must decide what to do with Beckett and her rapidly developing child, Liam Kincaid. Rayna transmits a signal to the Jaridians, an alien race. A Jaridian replicant probe assassin is sent to destroy the Companions. While attending Boone's funeral the leader of the Taelon Synod , Quo'on, is assassinated, but Liam saves Da'an. Da'an appoints Liam as his personal protector. Zo'or realizes that if Da'an is also killed, then he'll made synod leader by default.
The Taelon Commonality is hacked into, severing Da'an's connection with the Commonality. This causes Da'an to regress into a pre-historic version of the Taelons, an "Atavus". Da'an/Atavus is a threat and Zo'or orders Sandaval to kill Da'an for the Atavus hungers for life energy. The Resistance try to save Da'an.
Liam jumps through a Taelon portal which takes him two days into the future, at an exhibit of Taelon items from Strandhill, while in this future he finds the Resistance headquarters with everyone murdered . when he returns to the present, he races to find out who the assassin is and avert the massacre, but soon suspects that he himself is the assassin. zo'or beams brain wave emissions from the Taelon mothership down to liam, trying to destroy liam.
And Doors, now highly suspicious of Liam, becomes agitated and demands that Liam be shot on sight.
when their shuttle flight is sabotaged by Doors, Liam and Augur are thrown into a parallel dimension a woman called Maiya captures them and brings them back to The Imerian Resistance camp, while they find counterparts to people they know. The Taelons parallels capture the colony and imprision them on the mothership.
Augur is arrested for treason in Russia and condemned to death by hanging. However, he is blackmailed into participating in a Taelon experiment as advanced warriors and is given implantsI. Sandoval's attention is brought to Maiyal after she mistakes him for her husband "Jason". Liam helps Augur break his programming and brings him back from the rage. Lazarus, the overseer of the program, starts to feel himself after an encounter with Da'an and has some plans of his own.
While Maiya fears for her secret and so must find a plausable identity which will bear up under scruitiny, and drops a bombshell about Lilli and Isabel Martinez.
A Jaridian probe crash lands and disrupts the Taelon commonality , The Taelons begin to round up those suspected of being Resistance members, they take them to the mother-ship. The Taelons need a substitute to the commonality energies and so put the "suspected Resistance" into near death state but they wont be able to keep the Taelons going long. As Augur, Maiya and the others lie near death, Their souls in their own personal heavens Liam trys to save them by going in to a comatose state at great risk to himself, though getting the resistance members to leave could be hard. Lili and Sandoval try to locate the probe.
A technician Working on the New York to Bangkok inter-dimensional link is killed. creatures from another dimension that have an appetite for energy start appearing all over the world. Liam and Augur suspect the creatures may be from another dimension, and will drain every energy source on earth. The mothership becomes infested with the creatures, leading the Taelons to put themselves into a near-death state to protect themselves.
While climbing in a cave, Beckett falls. Unconscious, she hallucinates she is on trial for her crimes against humanity and for collaboration with the Taelons. Liam and Augur try to find Beckett before Sandoval finds and kills her. because her CVI has started breaking down.
Maiya and Isabel begin to suffer from dimensional phasing, Augur has a plan to help but it will mean that Maiya and her counterpart Isabel must merge or they may both die. To challenge the Taelons Doors enters presidential race. Lili and Isabel share stories about their fathers to a intresting conclusion. Sandoval questions Maiya onboard the mother-ship, while Doors and Zo'or discuss joining forces.