When nanites - tiny, self-replicating robotic spies - are discovered in the Warehouse, Claudia deduces that Sykes planted them in order to hack into a file called Atlas 66. Myka is itching to get into the field to neutralize Sykes and demands that Jane reveal the contents of this heretofore Regent-only file, but Jane puts the kibosh on the inquest - the Regents have a plan in motion and all agents are to stay put.
But Myka, Pete and Claudia can't sit still while someone targets everything and everyone they love. A clue from Claudia's surreptitious decryption of Atlas 66 sends Pete and Myka to a nearby high school, where they discover a woman who looks exactly like H.G. Wells. It's soon clear that this woman has none of the malice or cunning of H.G., but while Pete and Myka try to deduce what Sykes would want with this human anomaly, Sykes's henchman arrives. Myka secrets H.G., who says her name is Emily Lake, away to safety while Pete engages Sykes's right hand man in a battle that ends with the villain plummeting to his death from a fifth-story balcony.
But when Pete reunites with Myka and her charge, the women are in the sights of their former partner, Jinks, who is soon joined by the recently deceased henchman. While Pete and Myka try to wrap their brains around the devilish pairing of their onetime friend with a possibly immortal murderer, Jinks blasts them both with a Tesla and smuggles H.G. to Sykes's lair.
Though Artie's ready to rip his agents to smithereens for disobeying him, Jane reminds them that there's work to do. She explains that the hologram of H.G. that helped them with a previous case was separated from the body of H.G. - the Regents wanted to give the brilliant woman a chance at a new life, so they created two women - one physical, one metaphysical - with the help of an artifact called the Janus Coin. Once Sykes realizes that Emily Lake possesses none of the knowledge or skills of Wells, he will surely seek the Coin.
Once they have it in their possession, Pete proposes a radical plan to save the Warehouse: Since Sykes needs the Coin for his endgame, the Coin must be destroyed. Myka protests, as destroying the Coin means destroying H.G. But when Claudia summons H.G.'s consciousness, the literary genius insists that Pete go forward with his plan.
But Jinks and his cohort halt Pete in his tracks. They steal the Coin, but not before Jinks slips Claudia Sykes's whereabouts - Jinks has been undercover the whole time. Jane confesses that this was the plan she alluded to, and the agents rush to the secret location to save their friends, and possibly the world.
An empty airplane hangar rings with desolation and defeat: Sykes has escaped. But the loss of the Coin and H.G. feels small when Claudia discovers Jinks, lying murdered in the emptiness of Sykes's hideout.