Beckett get 'sucker punched'
When an enforcer for the Irish Mafias turns up dead, evidences reveals that the victim was killed in almost identical fashion to Beckett's mother. Castle lets Beckett know that he will do whatever she asks, including nothing. But Beckett wants his help to find whoever killed her mother. The killer is revealed to be the Irish mobster's own brother, going under the alias of Rathbone.
When Rathbone takes Castle hostage at the precinct, Beckett is forced to shoot him dead, effectively killing the only link to who ordered her mother to be murdered. Castle is contrite and offers to leave her alone for good. But Beckett refuses his resignation. She's gotten used to him pulling her pigtails and having Castle around at such a high stress job makes its fun. We knew she'd admit to liking him one of these days.