: Jane faces an Internal Affairs investigation and public exposure of her relationship with Agent Dean. Additionally, her past with Lieutenant Rafael Martinez resurfaces when he returns to Boston for a joint investigation. Key Episodes and Cases
: Deals with the immediate aftermath of the Paddy Doyle shooting and Jane’s departmental scrutiny.
: The season concludes with high drama as a building collapse traps characters inside while personal issues, like Casey Jones’s spinal surgery, come to a head. List of Season 3 Cases | The Rizzoli and Isles Series Wiki
: A central arc involves Maura’s search for her biological family. Jane eventually helps Maura connect with her biological mother, Dr. Hope Martin.
: The season opens with a severe rift between Jane and Maura following the shooting of Maura’s biological father, crime boss Paddy Doyle. Tensions between the two cause significant stress for their colleagues and family as they struggle to reconcile their professional duties with their personal loyalty.