1x11, "All The Way" - Nikita's backdoor in Division's computer network is liquidated, Thom is Killed Off for Real and framed as Nikita's mole, and Alex is promoted to field agent.
1x16, "Echoes" - Michael figures out that Alex is Nikita's mole and where Nikita's base is. Cue a month of reruns.
1x17, "Covenant" - Michael discovers that Percy is the one who ordered his family's deaths, which leads to him turning against Division and allying with Nikita.
1x20, "Glass Houses" - Jaden is killed by Nathan while fighting Alex, and a hidden recording device on her allows Amanda to finally discover that Alex is Nikita's mole.
1x21, "Betrayals" - Percy reveals that he's known about Michael and Alex's true loyalties all along, has Michael locked up, and turns Alex into a Double Agent by revealing that Nikita was the Division agent who killed her father. On top of that, he also reveals that he let them capture his third Black Box, because it's a Trojan Horse and part of his move against the government. And the episode ends with Alex shooting Nikita.
1x22, "Pandora" (season finale) - Percy's plan is narrowly prevented, but he still manages to destroy Nikita's loft, sending her and Michael on the run, but with a fully decrypted Black Box. Meanwhile, Alex cuts her ties with Nikita and Division, but is captured by Oversight, who want her to work for them.
2x10, "Guardians" was the first real wham of the season, as it reveals in its last few minutes that Alex's mother is still alive.
The two-parter "Sanctuary"/"Clean Sweep" (2x12 & 2x13) ends up quite effectively shaking up the status quo. By the time it's done, all but one member of Oversight is dead, allowing Amanda to take Division rogue again; to retaliate, the remaining Oversight member (Sen. Madeline Pierce) allies with Nikita's group, offering them presidential pardons in exchange for their help. Meanwhile, Percy's escaped imprisonment to plot his revenge, and the final scene reveals that Amanda is in a secret alliance with Ari Tasarov.
2x18, "Power" changes the status quo again — Percy retakes control of Division, while Amanda and Ari are forced to go on the run.
2x23, "Homecoming" (season finale), changes the status quo again in a big way, leading to a Re Tool the following season. By the time it's done, Percy and Roan are dead, Team Nikita is running a collectively Heel Face Turned Division, and a still free Amanda is shown to have decrypted the last remaining Black Box.