- With Michael's help, Nikita survives Section One's assassination attempt on her, but Section One believes that she is dead. While working as a waitress, Nikita is kidnapped by the Freedom League and taken to the terrorist group's headquarters.—Anonymous
- "Nikita: lost...and found. She's vanished, escaping Section for a return to the workaday world. But when Freedom League kidnaps her, Michael develops a bold plan to bring her back to a life of spying."
The first episode of Season Two begins with Michael overseeing new recruits' training. He is not paying attention and is remembering Nikita. A woman with long blonde hair walks in and for a moment, he thinks it is her. Of course it isn't, but nearly seeing her causes Michael to show undue aggression toward one of the recruits; he breaks his leg.
Madeline and Operations are watching from Operations' office. Operations tells Madeline that he got over Simone; he'll get over Nikita. Michael goes to his office and resubmits the message, "Nikita, are you there?" The camera pans back from the message to show an apartment with food, art, etc., ending with a shot of sunglasses strung on a line (Nikita's favorite thing from her old apartment).
Operations briefs the team on the latest attacks from Freedom League, the organization Section was fighting when Nikita "died". He mentions that the attacks are probably in retaliation for Section blowing up their building from the end of Season One. Walter makes a pointed comment, saying, "We all remember that," and looking at Michael. The briefing continues and Operations says that all teams will report to Ackerman. Michael is surprised he is not leading the teams.
Michael goes to Thailand, where Section believes they will find information on Freedom League. Michael drops trackers on the floor and the terrorist steps on them, allowing Birchoff to tell Michael where Sherrin (the boss) is. Michael waits for Sherrin to come out of the room and escorts him from the scene back to Section.
Nikita has been waiting tables in a diner. A customer is harassing her; he grabs her arm and tells her he doesn't like her attitude. The cook steps in and makes the customer let her go. Later, a new customer comes in. Nikita looks out the window and sees his buddies waiting outside. He grabs her arm and tells her to come with him. When they get outside, she sneaks an attack on him, kicks his buddy down the stairs and runs. She is cornered by two other men, who grab her and throw her in the van.
Next, she is shown being forced to walk down a dark tunnel with a burlap sack over her head. She is forcibly sat in a chair and she meets Freedom League's leader. He records a video of himself with her for Section to see. He wants them to know he has a hostage. After the recording is done, he tells Nikita that they have been looking for her ever since one of his men saw her escape from the building before the explosion.
One of his men interrupts his conversation with Nikita and reports that, "He just called." Section has a mission planned the next night. The leader tells his man that the more people Section sends, the more will die. He tells one of his other men to take her to a room where she will be locked up.
Madeline has finished interrogating Sherrin, who has given her locations of some of Freedom League's places. Operations wants to wait until Section can attack Freedom League's headquarters. He tells Ackerman to get ready (again, instead of Michael).
The man assigned to escort Nikita to the room attempts to rape her. She tells him she can make it easier for him by having sex with him mutually. As he's distracted by her smile, she whips her arm out and cuts his throat. He dies immediately and she prepared to escape. Her reflection is shown in the mirror she broke in order to get a piece to kill him with. Nikita finds a grate that she can exit through and sneaks out. She sees Freedom League's men preparing for their attack on Section's mission.
Michael is on a mission in France, the one Freedom League plans on ruining. As the car he is in pulls up to the guard house, Michael sees something and tells the other operative to get out of the car. The other man cannot get out in time and is blown up by Freedom League's men. Michael shoots the man who blew up the car, but is outnumbered by the other men. It looks as if he is about to die when someone shoots the Freedom League men. Michael turns around and Nikita is standing on the other side of the burning car. Michael is stunned. However, he is momentarily distracted by the comany's security personnel coming out of the building and when he looks back again, Nikita is gone.
Operations wants to know if Michael saw anything on site that would help them figure out who has been feeding Freedom League information. Michael tells him he saw nothing and then goes back to office to once again check for replies to his, "Nikita, are you there?" message. There is now an answer: Yes.
The scene changes to Nikita in a ship of some kind, waiting. Michael comes in and she pulls her gun. It looks at if they're about to fight when suddenly Michael begins kissing her. He tells her that he thought he lost her. She tells him he never had her and they kiss again. After the sex, Nikita and Michael talk. She tells him how she used to dream of being free of Section, but when she finally got out there, it wasn't what she'd expected. The next morning, Michael offers to bring her back in to Section. He tells her that after the explosion, he'd begun to believe she had died and that when he saw her in France, it brought him back. She asks what they're going to do now and Michael tells her he doesn't know.
Michael goes back to Section with information about Freedom League that he got from Nikita, claiming he got it from a contact in South Africa. Operations and Madeline tells Michael that Nikita is alive and show him the video the leader had made. Michael wants to know if Section is going to rescue her. Madeline tells him that they'll try. Michael asks Birchoff to do something for him and finds out that Ackerman has had all the codes changed, that he doesn't trust anybody.
During Ackerman's brief, Michael begins subtley challanging Ackerman's authority by pointing out flaws in his plan and suggesting alternative solutions. Michael then goes back to his office and texts Nikita, telling her he's found a way for her to be brought back to Section. At van access, Ackerman's team is ready and he says he will be right back. Michael heads him off and prevents him from sending a warning to Freedom League.
While Michael and Ackerman's team are moving through the Freedom League headquarters silently taking out its members, Nikita sneaks back in through the grate she escaped from. Michael and the other team members take out the leader and place explosives in the building. Ackerman orders them to evac, but Michael stays behind to rescue Nikita. When he finds her, he has to beat her up to make her look like she's been abused by Freedom League. He wants to stop, but she makes him do more damage so Section won't suspect them. As the van is about to leave, Ackerman orders the charges ignited. Michael escapes with Nikita on his back just in time. He comes into the van and Birchoff is happy to see her.
Operations and Madeline examine Nikita's medical file and are confused by her fresh bruises. They briefly suspect she was a willing informant of Section activities for Freedom League, but are quickly dissuaded from the notion by Michael who presents evidence of Ackerman's betrayal. He is quarantined in a room and Madeline explains everything to him: that he will debriefed and then cancelled.
Michael goes to visit Nikita in her hospital room. Michael tells her that she will be transferred to reprogramming to make sure she can still perform and that someone else will be her mentor. She wants to know if she and Michael can continue to see one another. He doesn't answer her. She tells him about a "dream" she had last night, reminding him of what he said to her on the ship. He tells her, "Sometimes all we have is our dreams." Nikita points out that he went to a lot of trouble to bring her back to Section and she wants to know why. He asks for her to be patient and leaves.
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