As Castle gives Beckett her bracelet to celebrate her first day as Captain, she gets a mysterious phone call from Vikram Singh using a classified code from the Attorney General that means life or death. Not knowing anything else, Kate lies to Rick to protect him and heads out to meet Vikram at the theater where she ends up getting shot.
As Beckett stitches herself up at the dry cleaners, Vikram explains that a search Beckett initiated two years ago about Senator Bracken and any links to criminal activity suddenly uncovered a classified document with the term Locsat 2011 BD. Vikram, an analyst forwarded it to McCord and less than 12 hours later her entire team was dead.
As an assassin team is about to kill Beckett and Vikram, another agent saves them. She says her name is Rita and she is has been married to Jackson Hunt (Castle’s father) for ten years. She thinks Beckett should make a run for it but Beckett insists on staying.
Beckett visits Bracken in prison and he tells her she’s uncovered something huge. He’s surprised she’s still alive and her visit to him will most likely lead to his death. Later, he is killed in prison.
Alexis and Hayley manage to track Vikram and get a view of his computer through security footage. They see the document with the term Locsat 2011 BD.
Allison Hyde from the AG’s office comes to the 12th to help with the investigation and contacts Castle to try and find Beckett but he doesn’t share the new information.
Although apart, Castle and Beckett both figure out that Locsat 2011 BD leads to an aircraft. Bracken had a mole in the CIA which helped him covertly move drugs via air into the US to fund his presidential campaign. Castle saves Beckett at the aircraft hangar when it looks like Vikram is about to shoot her. He wasn’t, he shot the pilot who was about to shoot Beckett.
Castle and Beckett kiss and head back to the 12th where Castle tells her how angry he is that she lied to him. She says she understands and that she was angry when he was missing for two months but she trusted him. She explains she was only trying to protect him. He tells her they can get through anything if they do it together.
Castle and Beckett plan a trap at his office and Esposito and Ryan help take down the assassins. When another comes in holding Hayley at gun point, Castle uses his hidden gun in his desk to take him out and save the day.
Everyone celebrates as Captain Beckett comes back to the 12th until they realize that Agent Allison Hyde was part of the cover up. When they finally track her down, she’s committed suicide. Rita tells Kate that Allison was just a patsy but her death will keep Beckett safe but Beckett can’t let it go. She wants justice. Rita points out that she can either dive back down the rabbit hole or she can have her life with Castle but not both. If she continues to investigate this case she may get them both killed.
Back at the loft, Castle is making them smorlettes when Kate tells him she needs time away to figure things out. She takes her bag and leaves.