Ziva and the Bodnar arc
28 episodes of NCIS carry this thread, 1d 4h in all — 11 of them are in The Essentials.
Arc membership is derived from each episode's own title and summary text. It shows where a thread is foregrounded, not every episode it touches.
In airing order

When the bodies of two assassins are delivered to NCIS from overseas, Tony and Ziva assume their identities undercover and engage in a sexy rendezvous at a luxury hotel in order to find their target.

Gibbs and the team rush to find Tony and Ziva who disappear while investigating a shipyard for smuggled weapons.

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

With Gibbs retired and boat-building in Mexico, the NCIS team must learn to work without him when Ziva is wanted by the FBI after she witnesses a political assassination.

Ziva's undercover assignment takes a shocking and deadly turn when the serial killer she has been tracking becomes suspicious of her.

When a former NCIS Special Agent is found dead in a swimming pool at his home in Los Angeles, Jenny, Tony and Ziva travel to Los Angeles to attend the dead Agent's funeral. An encounter at the dead former agent's memorial service has Jenny greatly unnerved and soon realizing that the agent's death may not have been natural after all, prompting her to bring in an ally of the NCIS team to help out. As Jenny and Mike dig deeper into the case, they're unaware of the fact that the same group of assassins that killed the NCIS agent are after them while Tony and Ziva attempt to find Jenny who has ditched them while they were in Los Angeles but tragedy lies in wait and it's something that threatens to change the structure of the NCIS agency forever...

The body of a Marine leads Gibbs and McGee to the NCIS OSP division in Los Angeles, where a murder investigation quickly climbs to a matter of national security in which the two offices must work together to resolve. Meanwhile, Tony begins to snoop into Ziva's personal life.

With the appearance of Mossad agent Michael Rivkin, Tony is forced to question Ziva's loyalty to NCIS. Meanwhile, in Los Angeles, Special Agent Callen goes undercover to try to catch a terrorist cell while OSP psychologist Nate Getz discovers the startling truth about Gibbs and Special Agent Lara Macy's relationship.

Ziva's homecoming to Israel with Gibbs and the team is not a happy reunion with her father, the enigmatic and powerful head of Mossad. As tensions rise, Gibbs is forced to make a decision that sends shockwaves through NCIS.

As the hunt for Ziva's replacement begins, Gibbs and his remaining team members must head back to work with the past still weighing heavily on their minds.

When a Marine's body surfaces halfway around the world, the investigation forces Ziva to dig up a buried chapter of her life.

When a Marine known for his practical jokes is found dead on Halloween eve, the NCIS team discovers that the victim's "good-natured" pranks may have inspired ghoulish retribution. Meanwhile, Ziva tries to adjust to her new role on the team.

The team is assigned to protect Ziva's father, when his attendance at a NCIS conference leads to some unexpected surprises.

To Gibbs' displeasure, Special Agent E.J. Barrett returns to lead the investigation of a seaman's death that may be connected to a series of port-related murders. Meanwhile, Ziva finally introduces her boyfriend, Ray, to the team.

As the NCIS team continues its search for a missing Marine, Gibbs and Ziva travel to her last known whereabouts in Afghanistan. Meanwhile, Tony reveals his deepest fears and Gibbs is forced to relive events from his past.

When a Navy lieutenant commander is found dead in a building under construction, NCIS must search for a killer while dealing with interruptions from her distraught detective husband. Meanwhile, Ray's return has Ziva thinking about her future.

Following the murder of a Marine, Tony and Ziva join Ziva's longtime friend and mentor in Columbia in a search for a missing Marine Lieutenant and Navy Chaplain. Meanwhile, Jimmy Palmer decides who will be his best man.

The NCIS investigation of a fire on a Navy vessel reveals evidence that elevates security at all U.S. Navy facilities worldwide. Meanwhile, DiNozzo and Ziva travel to Italy when an explosive device is found hidden on a Navy ship.

When a helicopter crew is adrift at sea and later discovered on shore, the NCIS team must determine the cause of the crash and locate the missing pilot. Meanwhile, Tony and McGee channel their inner "Maverick" and "Iceman," a la "Top Gun," and Ziva challenges them to a dare.

Gibbs continues to work with Captain Wescott while he retraces his steps in order to help the NCIS team track down a terrorist. With Thanksgiving on the horizon, Abby's enthusiasm for the NCIS family dinner is building, and Tony's curiosity is peaking when he learns Ziva is making special plans for the opera.

As the NCIS team investigates a teenage girl's abduction, Ziva and Abby work closely with her young friend who witnessed the kidnapping. As the investigation unfolds, Gibbs seeks help from a past contact, Miranda Pennebaker, a well-connected woman with questionable morals. Meanwhile, Tony gets jealous when he learns Ziva is making plans with a mysterious man.

While the NCIS team investigates the link to a dead journalist and a Navy petty officer, Ziva is taken aback by the sudden emotional visit by her father, who she hasn't seen in more than two years. While Ziva questions the purpose of her father's visit as the Director of Mossad, her father insists he is in the U.S. strictly to see his daughter for Shabbat dinner.

When a Navy reservist returns home to find her husband missing and her living room covered in blood, she turns to the NCIS team to bring him home. Meanwhile, Tony suspects that Ziva is planning a risky move to avenge her father's death.

While the NCIS team investigates the murder of a Mossad officer in Virginia, Tony and Ziva depart for Berlin as they track her father's killer.

In retaliation for the murders of Eli David and Jackie Vance, the NCIS team feverishly searches for Bodnar despite orders from Homeland Security to relinquish the case.

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.

Determined to locate Ziva, Tony chases leads in Israel in search of her current whereabouts. Meanwhile, Gibbs and the team continue the hunt for Parsa and his growing terrorist ring.