Nikita takes off from Division to kill the President in order to protect Michael. As she leaves, Michael tries to stop her. She tips him off that Amanda is listening in. The team figures out what Nikita is going to do. Birkhoff blocks Amanda's listening device and Michael and Alex try to convince her to stop. Nikita tells Michael he's been infected. Alex suggests they find the inventor and get an antidote.
Nikita continues on to the White House and they head to find the doctor. Nikita is met by a Shop plant, Sterling, and he gives her a gun. Nikita goes into the Oval Office and starts to explain what's going on to the President. She gets interrupted by Michael. He lies to her that they got the antidote and she doesn't have to go through with it. The Shop infected and then monitored the doctor and when he found out about how his research was used, they activated the nanotoxin and killed him.
Nikita warns the President that people, including those in her inner circle, want to kill her. She says she's aware of that. Nikita put the gun on the desk. The President picked it up and shot herself in the head. Nikita was shocked. The Secret Service come in and take Nikita into custody and take her through the tunnels. Sterling meets them and orders them to hand her over. When the officers refuse, he kills them. Amanda and the Shop want Nikita dead so she can't reveal what happened. Birkhoff hacks Sterlings ear piece which gives Nikita a chance to take him out. She kills him and escapes through the tunnels.
In order to save Michael from the nanotoxin, Alex suggests that they kill him and then revive him like Amanda did to deactivate her kill chip. Michael agrees and he's "killed" just in time. Amanda triggers the nanotoxin, but it fails. She has a back up plan and sends the remaining Dirty Thirty members in to kill everyone at Division. The team nearly loses, but Nikita shows up to kill off the remaining infiltrators.
She goes to see Michael and they continue to have trouble reviving him. He comes around and officially joined them in the killed-and-brought-back club. They leave Division and Nikita triggers the explosions to permanently destroy Division.
They go to a hideout and plan next steps. Nikita doesn't want to put them all in the position to help her. They want to help her because they care about her. They start planning with Alex is going to become an UN Envoy to give them access to different countries with Shop locations, while doing good as Alexandra Udinov. Then, they realize Nikita left. She takes off to handle situation on her own, even leaving her engagement ring behind.
Meanwhile, it's revealed that the President isn't dead. An impostor committed suicide. They abducted the President during the G-6 in Toronto.