The scenes of the "Factory" (actually just one labor camp in a whole gulag-complex of them) in 2035.
The reveal that the CMR remains operational and can be remote hacked by someone to find out the user's location and see through their eyes, even after the user's death.
The similar reveal that the CMR can be hacked to perform Laser-Guided Amnesia on individuals, without them even being aware that certain memories have been erased. Such as what Future Alec did to Kiera in 2077, when she came close to discovering the conspiracy.
And in the 2060s and 2070s, the Corporate Congress's military divisions routinely did remote-control overrides of soldiers to make them do things they wouldn't normally do. Kiera could've been made to kill anyone, even her own family.
Due to the CSIS badge preventing anyone from ticketing or towing his car, no-one discovered Agent Gardiner's corpse in the boot for nearly a month.
The season 2 finale. All the time travelers, meaning Kiera and the Liber 8 members (including the dead ones) are locked up in individual cells in an underground bunker by the Freelancers, where by all indications they are just going to be left to rot. Oh, except for Chen, who is one of the Freelancers, and seems to have somehow survived being killed.
In Series 3 premiere, the reveal that changing the past can cause reality to break apart for those still living in the timeline that was left behind.
Alec's efforts to destroy the second CPS are essentially meaningless. Even if we assume he finished the job, Kiera's dead double just provided a replacement, so Travis could still get his hands on it. And there is now a second time travel sphere.
Even if Kiera does restore 2077 and goes back to it to regain her family, it is still NOT the family or world she left. Too much has happened for it to completely resemble the time-line she came from, to the point where there's no telling if her husband and son would still exist. And even if they did, there's still the problem of that time's Kiera. So, unless she completely undoes all the changes somehow (making the entire show moot, likely by sabotaging the time-travel device to kill Liber 8 at the execution instead of working correctly), her original family is outright gone. Kiera herself has realized this in "The Dying Minutes".