A CVI malfunctions and kills a soon-to-be father. The investigation leads Liam and Renee to a fertility clinic. Renee finds out she is infertile and suspects that Taelon technology is affecting worldwide fertility.
Da'an leaves and doesn't being Liam along. Zo'or is frantic as to why Da'an left. Liam wants to help but Zo'or doesn't trust him because he doesn't have a CVI, so Liam agrees to be implanted. But his CVI enables Zo'or to see and hear what Liam does. So he tells Renee. She tells Street who comes up with a plan to make double of Liam which doesn't have a CVI so with the double they try to find Da'an.
When the mother ship hits dark matter, the ship dos not begin to heal itself. Zo'or is left in an unconscious state and Sandoval takes control. He decides it is time to liberate the Earth from the Taelons.
Sandoval is watching via nanobots inside Street as she tries to decipher Ma'el's riddle. She tries to figure out how to escape from Sandoval and the Taelons forcing her to solve the riddle. She flashes back to childhood fears.
Liam and Renee learn of a facility where time travelers from the future are being held. They try to learn from them what happens to the Taelons. Sandoval's wife is used as a pawn to gain important information from him.
Sandoval goes to Renee to request a trial to testify to atrocities against humanity committed by the Taelons. A manhunt for Sandoval begins when he quits and leaves the mother ship. Liam has to protect him on his way to the grand jury.
Strange assaults and several deaths may be related to a Doors/Taelon joint venture where Taelon core energy was used to heal people. It appears that the energy is being sucked back out of the patients.
When Renee's boyfriend appears to her while he is imprisoned on the mother ship, Liam theorizes a special energy bond between the pair. Zo'or is upset by the human's betrayal and bans all humans from the mother ship.
The Taelons announce that they will all go into death stasis and wait on the mother ship for humans to discover how to create core energy and revive them. Zo'or and Da'an don't trust each other to be the last to submit to stasis.
Eight Taelons are killed when protectors' implants are re-calibrated with a new imperative to kill instead of protect Taelons. They fear the Jiridians have found a way to control the CVIs. Meanwhile, their core energy continues to deplete.
When Street solves the 8th dimension of Ma'el's riddle, a beacon leads Liam to a chamber with a healing pool. However, there is only enough in the healing pool to help 6 Taelons. Zo'or will do anything to insure his own life.
Renee has spent company money and time on a search and rescue team to discover what happened to Liam in the chamber. She is asked to cease or quit. She quits, convinced that Liam is alive. Street helps her put together a new search team.
On the mother ship, Sandoval tries to deal with the Atavus to preserve himself. Renee wants to act, tries to convince Hubble that the Atavus exist and need to be terminated. Street doesn't trust Hubble and thinks they should just lay low.
Renee is still having trouble getting anyone to believe her about the Atavus. She meets a man who tells her that people who live underground are disappearing, due to the Atavus. They find a chamber used to make hybrids.
Renee has crystal that shows a map of where all the other Atavus hives are throughout the planet. She goes to Boone for help in destroying the hives before Howlyn can find them. Sandoval resurrects Zo'or to hunt Boone.
From a hive under Stonehenge, Renee and Street take an Atavus called Gren in his stasis chamber to the Antarctic to see if the cold will affect him. Gren tries to convince Street that most Atavus are peaceful and will not feed from humans.