The Human Factor
When Homeland Security inexplicably seals the crime scene of a car bombing, Castle and Beckett find themselves with two mysteries on their hands: who murdered the victim, a government whistleblower, and why are federal agents trying to take over the case? The plot thickens when they discover that the victim wasn't killed by a car bomb but by a missile from a military drone. Carlos Bernard guest stars as Jared Stack, a mysterious operative who may hold the key to solving the case.

Watershed
In the season finale, an interview with a high-profile federal law enforcement agency forces Beckett to reconsider what she wants out of her job and out of her relationship with Castle. Meanwhile, the body of a young woman is found floating inside the water tank of a skid row flop house, but as the team investigate, they discover that her final resting place is just one of many strange things about her death.