EPISODE 12 – "The Box, Part I"
News her mother was KGB is too much for Sydney, and now she wants to resign from SD-6. Suddenly, heavily armed intruders led by McKenas Cole take control of the building to torture Sloane for access to the vault, triggering explosive lockdown measures. Forced to the basement Jack and Sydney must think fast to avoid the total destruction of the building.

EPISODE 13 – "The Box, Part II"
Vaughn disobeys orders and attempts to help Sydney and Jack avert the destruction of SD-6 headquarters and all its occupants, as McKenas Cole continues his vendetta against Sloane and searches for a mysterious device. Meanwhile, evidence and a desperate but determined woman convince Will to continue his investigation of SD-6.

EPISODE 14 – "The Coup"
Sydney and Dixon are sent to Las Vegas to gather information from a K-Directorate agent who has ties to the group that attacked and nearly destroyed SD-6. Sydney learns some shocking news about Fracine's fiancé. Jack continues to try to be more of a father to Sydney when he helps her decide whether or not to continue with graduate school.

EPISODE 15 – "Page 47"
Sydney returns from an SD-6 mission in Moscow with a video of the mysterious Mr. Sark's meeting with K-Directorate. Vaughn asks Sydney to use her friendship with Sloane's wife, Emily, to gain access to a mysterious Rambaldi book. Meanwhile, Will's life begins to spin out of control when he is kidnapped and told to drop his investigation of SD-6 or risk the lives of his family and friends.