Starting with one word - Nightingale - from Bill Vaughn's journal, Syd discovers its connection to Dr. Josef Vlachko. She also finds that he's currently working with Hans Dietrich, a money launderer involved in weapons sales who funneled over a million euros to an account labeled Nightingale. Syd presses on with the search.

A wary Sloane asks Jack how much Sydney and Vaughn know about Project Nightingale. Jack suggests that they tacitly let the pair continue the search.

In a rogue operation, Syd and Vaughn go to Dietrich's beer hall in Munich. Dressed as a beer maid, Sydney charms Dietrich. Then they go back to his private office where she beats him and rips out the hard drive from his computer. As guards arrive, Syd and Vaughn fight their way out.

Back in Los Angeles, Vaughn secretly meets with a mysterious man named Roberts, who knows about their "trip" to Munich. Roberts says he'll give Vaughn info about his father in exchange for the transformer coil from Project Nightingale. Vaughn agrees, though he doesn't yet know what Nightingale is. Before he leaves, Roberts gives him his contact information and the name "Philip Burke" as a lead.

Jack invites Sydney out for dinner to learn more about their acquired intel. Sydney says that Vlachko is running Project Nightingale in an abandoned nuclear plant and using humans as test subjects for experiments. Jack tries to convince Sydney to bring this intel to APO.

Sloane tells Jack that due to Vlachko's ties with Elena Derevko, he needs to send a strike team to Siberia. Jack says they should wait for Sydney to willfully bring this to APO. Once she does, Jack will join the mission so he can interrogate Vlachko without Syd and Vaughn's knowledge. Sloane advises Jack to eliminate Vlachko because he can alert Elena about their agenda-or worse, talk to Sydney.

Vaughn tells Sydney about Philip Burke: he was killed the same day that Bill Vaughn was supposedly killed, and his dental records are identical to Bill Vaughn's. Vaughn also says that he met with Roberts, who wants the transformer coil. Syd suggests they bring this operation to APO, then acquire the coil through a rogue countermission. After they report to APO, Jack says that he'll join them in the retrieval of the transformer coil.

After infiltrating the Siberian nuclear facility, Jack shuts down security while Vaughn and Sydney run toward the test chamber. Sydney enters the chamber to retrieve the coil inside the nuclear reactor's containment shield. A guard arrives and shoots at Vaughn, destroying the control panel in the process. Syd is trapped inside as the nuclear reactor starts counting down. After Vaughn's failed attempts to stop the reactor, Marshall says another way to stop this is through the removal of fuel rods from the core.

Meanwhile, Jack finds and interrogates Vlachko. Upon hearing that Sydney's life is in danger, Jack shoots Vlahcko and heads toward the nuclear core to remove the fuel rods. Marshall advises Jack against this as he tries his best to bypass the system.

Suddenly, the nuclear reactor shuts down. Syd walks out the chamber and hands the coil to Vaughn. After they kiss, Vaughn punches Sydney and runs away with the coil as Syd watches him go. Sydney then goes to Jack and tells him that Vaughn took the coil from her.

Jack and Sloane discuss Sydney and Vaughn's deceit. Later, Marshall realizes that Jack shut down the reactor himself. Jack tells Marshall that his daughter's life depended on it and demands that his actions remain a secret.