Sara Pezzini is under investigation after the death of her partner, Danny Woo, at the Rialto Theatre. She finds out that her boss and friend, Joe Siri, will retire as Captain and Bruno Dante will head both Special Investigations and Homicide. After Sara leaves the room, Joe asks Dante to drop the investigation and let Sara stay on the force as a favor to him. Dante obliges, but warns Joe that he will owe him big.
She and her new partner, Jake McCartey, respond to a report of gunfire in Manhattan's lower eastside at around 11am. Three men on motorcycles are after Ian in a tunnel. Ian takes two of them out. The third comes out of the tunnel unscathed and shoots at Sara and Jake. Jake suffers a flesh wound. Sara takes a motorcycle from one of the men that went down and chases after the shooter. She loses him and returns to the crime scene.
Joe visits Sara at her apartment to say good-bye and to drop off a box that her father had left to her. Joe tells her that the box contains information that will help her find out who she really is.
Jake accesses the CIA website to obtain info on the current investigation. He finds out that the two men killed in the incident were part of an experimental warfare program known as the Black Dragons. The only two Black Dragons left are Ian Nottingham and Hector "Moby" Mobius. When Sara asks Jake whether he has any federal connections, Jake lies and says no.
Irons admits that Vorschlag was involved with the Black Dragons experiment. Irons tells Sara that the soldiers became out of control. Ian is the only exception. He embodied his ideal Black Dragon-both lethal and loyal.
Sara tells Vicky PO to examine a brain from one of the Black Dragons after Sara recalls Irons mentioning something about monkeys brains. The results show that the reptilian brain was unusually large, which made them highly intelligent and aggressive. Their turbocharged brains are also more sensitive to certain frequencies of sound and strobing lights. At the same time that Vicky is explaining to Sara about the examination results, Moby, knowing that Ian is following him, rigs his van with strobe lights. Ian tries to open the van and triggers sensors that activate the lights, causing him to go into a seizure. Moby then tranquilizes him and takes him to Irons residence. He uses Ian to gain access into the building. Moby wants to kill Irons because Irons couldn't control them and ordered Ian to eliminate the rest of the unit.
Moby ties both Ian and Irons up. During Moby's "poet warrior" speech to Irons, Ian manages to get hold of his cell phone to call Sara. Sara hears Moby and Irons voices and rushes over. Moby is armed with a blow torch. Sara arrives and shoots Moby before he can set the full blast of the blow torch on Ian and Irons. Despite his gun wounds, Moby stays on his feet and tries to torch Sara, but the Witchblade morphs from a gauntlet into full armor and protects her from the flames. She walks toward Moby and uses the gauntlet to stab him. Moby grabs her by the arm and pulls the sword deeper into himself. He tells Sara that she "slayed the wrong dragon" and falls to the ground and dies. Afterwards, Ian frees himself and then unties Irons on his own. Irons appears to have set up the whole ordeal so he can watch Sara with the blade and so she can kill Moby for him.