The new season of Continuum starts off with a bang as Alec is teleported back in time after diving into the time stream at Escher's labs. A bullet followed by one of the Freelancers follows him into the stream, grazing his forehead. Two very stunned lab technicians are surprised to see him there; they call for security as he flees the facility.
Back in the current timeline, Kiera and all the members of Liber8 remain prisoners in a remote holding facility, guarded by the Freelancers. Kiera is shocked to see that Curtis Chen is still alive; he takes into another room to interrogate her about not just where Alec has gone, but when.
Alec meanwhile in the new past timeline appears to have successfully traveled back one week prior to the confrontation with the Freelancers that killed Emily in the process. He buries half the time travel device in a park for safe-keeping, taking the other half with him. Alec shadows Emily in the new timeline and is shocked to see another, paradoxical version of himself. Jason catches Alec snooping on himself and offers to help.
Chen brings Kiera to meet Catherine, the "Keeper of the Cells" and apparently leader in charge of the Freelancers. Catherine explains to Kiera that when she left her own timeline in 2077, during the botched Liber8 execution, she disrupted history. Catherine outlines the thousand-year history of the Freelancers, or "Guardians of History" as she puts it. Kiera doesn't seem so convinced as accuses them of being a cult.
Catherine explains that the time continuum is like a tree; when Alec went rogue, he created a new branch of the tree, erasing himself from the current timeline. Thus, the future that Kiera so desperately wants to return to no longer exists, because that Alec Sadler never grows up to become the CEO of SADCORP because he longer exists. Catherine outlines that Kiera now has more in common with the Freelancers than she realized and that they must fight together to repair the damage done lest they all lose their futures.
Back in the new timeline, Alec and Jason team up in the lab as Alec forms a plan to save Emily. Kellog arrives unexpectedly. Without revealing his identity as a future version of himself, Alec lays out a grim picture for Kellog if Escher is allowed to fully develop his antimatter ventures (really, just a cover for developing time travel) and makes it clear that Escher won't hesitate to use that technology to kill Kellog and the rest of Liber8.
In the current timeline, Catherine propositions Kiera to help them restore the continuum. Believing them to be members of an insane cult, she refuses. As she is escorted back to her cell, she passes Garza as she's being escorted by a guard. The two women lock eyes for the briefest of moments and come to an instant understanding: they both overtake their captors and work to help each other escape. The facility goes on lockdown as the Freelancers hunt for the two time travelers.
Alec manages to give his past self the slip while reuniting with Emily. He proposes they run off to Thailand together (as she had suggested in his old timeline) and she agrees. Encouraged that his plan might actually work, he heads out to take care of a few loose ends - namely, Kiera.
As they flee, Garza and Kiera come to an understanding to help each other out; Garza will help Kiera escape so she can get the cops to come and raid the facility and save them all. As Garza attempts a diversion, she is shot and killed. Kiera flees but is cornered by Chen when her escape route runs out into a large spillway in a damn. As the two fight, they see the sky is exploding and flashing around them: their timeline is falling apart. Chen apprehends Kiera and drags her back to Catherine.
Catherine explains that the more Alec changes his new timeline, the more it destroys their current timeline. Their only hope now is to send Kiera back in time to correct the timeline to restore the future they all know. Kiera points out that if she goes back in time, everyone in this current timeline will cease to exist; it's a risk Catherine's willing to take as she knows that another version of the Freelancers will survive. Before Kiera goes back in time, they tattoo her hand with two dots: the mark of the Freelancers. Catherine warns Kiera to say away from the past version of herself, as the results could be unpredictable; they provide her with a newer, more advanced CPS suit and service weapon.
Back in the new timeline, Kellog meets up with Escher at an art gallery, as he did once in the past. When that meeting fell through, Kellog simply refocused his tech venture efforts on other targets; in this new timeline, as Kellog walks away, Escher is shot in the head by an assassin, revealed to be Emily just a few moments later.
Kiera travels back in time to the same location, but a week earlier. She goes to make her escape and sees Garza still imprisoned. Feeling as though she owes her for her death in the old timeline, Kiera frees a very confused Garza, who manages to escape from the facility. Chen and Miller capture Kiera, who willingly surrenders. When she's taken to Catherine, Kiera acknowledges there are now two Alec Sadlers in this timeline, and that Catherine herself sent her back in time to correct the continuum; Chen verifies this by scanning Kiera's Freelancer tattoos. In this new timeline of two Alec Sadlers, Kiera must decide which Alec will restore the continuum and do whatever it takes to stop the other Alec.
Back at the lab, Alec gathers his passports and other belongings to make a hasty retreat to Thailand with Emily, when he notices a pool of blood and a very dead Kiera Cameron lying on the floor with a single bullet wound in her forehead. He's overcome with grief just as he hears something stir behind him.
He turns, stunned, to see Kiera standing there, very much alive.