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14 episodes of NCIS carry this thread, 14h in all — 5 of them are in The Essentials.
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This page runs the whole series and shows episode details, including late ones. If you have not seen the show, start from the show page instead — the path reader hides what is ahead of you.
In airing order

The NCIS team rallies to clear his name when Tony is accused of murder.

When McGee kills a man while on assignment, the NCIS team steps in to back him when they discover the man was an undercover police officer.

Ziva becomes the focus of an NCIS investigation when a suspect in her custody dies.

When the dead body of arms dealer La Grenouille surfaces, the NCIS team is put under investigation for his murder by the FBI and Jenny Shepard becomes the prime suspect.

Department of Defense investigator scrutinizes the NCIS team's response to the Bodnar case involving the murder of Ziva's father and Vance's wife. Meanwhile, the team examines whether a Petty Officer is suffering from paranoia or if his claims of being followed are tied to a matter of national security.

The international manhunt for Eli David and Jackie Vance's killer turns into a federal witch hunt against Gibbs and the team, which questions their unconventional methods and threatens their future at the agency.

An explosion at a D.C. event that results in a casualty connected to the agency changes Parsons' perspective on Gibbs and the NCIS team. Meanwhile, without badges, DiNozzo and McGee investigate the case as civilians, despite the case's dangerous ties to each of them.

After a convicted felon swears the NCIS agency framed him for murder a decade ago, Gibbs begins his own investigation, starting with a new autopsy by Ducky. Also, Senior FBI Agent Fornell joins the team, since he was the lead investigator in the original joint FBI and NCIS case.

United States Secretary of Defense Wynn Crawford shuts down Gibbs' murder investigation and demands that Special Agents McGee and Torres be arrested for their actions in the case.

While pursuing a dangerous arms dealer, the team is shocked when Bishop is implicated in an old NSA leak. Also, Gibbs and Marcie realize the killer they've been tracking may be onto them.

When Agent Parker is framed for murder, the team puts their jobs and lives on the line to buy time and uncover the truth.

Special Agent Alden Parker is still on the run with his ex-wife Vivian, so the team investigates who from his past might have a personal vendetta against him in hopes of clearing Parker's name. Enlisting the help of NCIS: Hawai'i's Special Agent Jane Tennant and Computer Specialist Ernie Malick, who are in town meeting with Director Leon Vance in preparation for a global military exercise, the group tracks down their prime suspect, The Raven.

On her first NCIS: Elite mission, Knight is given orders to hunt down and arrest Eleanor Bishop after the former member of the NCIS team is designated a wanted cyber-terrorist. In need of someone to trust, Bishop turns to Torres, and the two come face to face for the first time since she abruptly left nearly five years ago.

The team races to help one of their own who has been framed for murder and caught in a widening conspiracy that could compromise national security.