The Shop's plan is revealed. They steal a Pakistan missile and hack into Pakistan's missile command center with Ramon's help. The head of the Shop tries to negotiate a deal with Nikita. She co-offers that they turn themselves in. When a Shop assassin attacks Alex, she questions him and finds out the Shop's true identity a military company, MKD. Phillip Jones is the CEO.
Amanda wants Birkhoff's father to destroy Shadownet. Instead, he reaches out to Birkhoff and discloses his location in Dubai. Nikita and the team heads there to stop them from launching a missile at the American sea fleet. When Nikita gets there, Jones orders the missile launch stopped, but Amanda goes ahead with it.
In order to protect the American fleet, Nikita has Birkhoff launch the missile they took from Ramon. Birkhoff saves his father and they find the American President alive. Nikita barely makes it out. Amanda died in the attack and Phillip Jones was arrested. Though, it turns out it was all a ploy. An imposter Amanda died in the missile strike and Jones wasn't really arrested. They complied with Nikita's demands.
Now, Nikita thinks the fight is over and they can continue their activities. Meanwhile, Alex found out that Sam was going to steal her diamonds. She gives him a briefcase of fake diamonds and sends him off telling him she'll play the role of a decoy.