Hot Owen is back! He leaks a Chilean assassination plot from the thumb drive Percy had once entrusted to him. His hope was that Percy would call in his mysterious "engineer" in order to fix the obvious design flaw in the whole black box system, who would then lead him to the other black boxes. Everything goes south quickly, so he enlists Nikita's help. Meanwhile, a peppy little CIA drone named Ryan is this close to uncovering Division's dirty secrets, so Percy and the drone's CIA boss decide to frame him for the assassination. Nikita, having received info on the frame job from Alex, warns Ryan, but Chilean rebels abscond with him into the forest. Owen, new to this whole "hero thing," follows Nikita's lead in rescuing Ryan. Michael is there with Division to stop them, but then the US military shows up to stop them. You see what happens when the right hand doesn't know what the left is doing? Division retreats and the military load Ryan and our would-be heroes onto a plane bound for America. Nikita convinces Ryan to help them escape and Owen seals the deal by giving him the thumb drive. They parachute to safety, and Ryan is exonerated. In his place, his CIA boss is framed and the whole machine keeps chugging along.
Back at Division, Alex is keeping tabs on that engineer. She spies on him as he teaches Birkhoff everything he needs to know about the black boxes and fixes the design flaw. Percy "promotes" Birkhoff by snapping the engineer's neck right in front of him. Alex sees the whole thing and realizes just what Percy is capable of. She's not the only one on spy duty: Jaden, suspicious of Alex, has started keeping tabs on her. On the one hand, it's good that someone notices how sneaky Alex is. On the other hand, Jaden continues to be annoying as hell.
Nikita's voice-over catches us up on what's been going on with Division and Owen and the black boxes. I sort of wish they would just do "previouslies" like on other shows, because these VOs are kind of clunky. Nikita has the Newark Community Center all to herself, so she takes a swim to the strains of a creepy choral rendition of Radiohead's "Exit Music (For a Film)." (Fellowshipper on the forum has identified it as the work of Scala.) After her laps, she sits at the edge of the pool, looking pensive. Maybe the music is bumming her out. A man in a dark hoodie watches her from outside, then approaches as she goes to towel off. She immediately springs into action, giving the intruder the towel-snapping of his life. He goes down without much of a fight. Before she can give him another lashing of her Egyptian cotton terry, he pulls back his hood and shouts, "Wait! Waitwaitwait!" It's Hot Owen, who really should have identified himself to start with. But yay! "What do you want?" Nikita asks, none too happy. "I started something," he says. "I need your help to finish it."
Cut to a news broadcast showing anti-American protests in Chile. A reporter says that video footage has been released, showing the assassination of Andres Quintana, a Chilean presidential candidate thought to have died in a car accident. Birkhoff's voice is heard talking to the operative who strangles Quintana in his car.
This has everyone at the CIA headquarters in a tizzy. A guy who looks like Chris Parnell leads a small gaggle of suits into an office, barking orders at them to figure out who was behind the operation. "Maybe it's Fletcher's 'ghost unit,'" one of the suits says mockingly. Fletcher, who's bringing up the rear of the group, seems very wee and delicate, but he earnestly tells the group about the "off book" operations he's been tracking since Mirko Dadich's murder. He asks for permission to return to Chile so he can hunt out this mystery group. "Like the dark matter of the universe, they fill in all the empty spaces." Everyone laughs at him and his crazy ideas. Fletcher looks like a kitten who's been denied a bit of string.