When an undercover FBI agent is killed in the field, the team makes the unnerving discovery that the identities of multiple undercover agents have been compromised, including Maggie who has been actively working to infiltrate an eco-terrorist group. Meanwhile, the team enlists the help of Special Agent Dani Rhodes, whose cover was also blown, to not only save their own but to aid in uncovering who was behind the leak.

When a famous rapper and two teen fans are gunned down on his tour bus, the team discovers there may be more to the story than his feud with another rapper. Meanwhile, Isobel hits a major milestone that has her contemplating her future at the Bureau.

After a young girl goes missing in Queens, the team discovers the kidnappers used her as leverage to carry out a major explosives heist, sending them on a hunt for the dangerous culprits. Meanwhile, Scola and Dani begin working on their footing as partners.

When a CEO is killed by a targeted explosion inside his penthouse, the team must work to figure out how someone accessed the highly secure building. Their task is further complicated when they discover the crime may be the work of an artificial intelligence program. Meanwhile, Maggie pumps the brakes on her personal life.

After Jubal narrowly escapes a calculated assault on a secret FBI office, the team discovers a rogue terrorist group has infiltrated the FBI. Unsure of who to trust, the team must work in the shadows to unmask the culprits threatening the sanctity of the New York field office.