3.01-3.02 "Kill Ari, Part I" and "Kill Ari, Part II"

The last appearances of all four characters from Seasons 1-2.

Ari goes after the women in Gibbs' life, using what happened to Gibbs' first wife and his daughter against him. Ziva and Gibbs set a trap for him, first in Norfolk, and then in Gibbs' basement back in Washington when that falls through. Ari tells Gibbs that he hates him because Gibbs reminds him of his father; Ziva shoots and kills Ari.

In Part I, Kate makes several very un-Kate-like appearances to her friends and teammates, appearing to each of them in ways that befit their differing personalities. (We'll leave it at that.) In Part II, she makes a few last appearances: one to Tony, amusedly commenting on his fear of Ziva, and one to Gibbs, who is late to her funeral after dealing with Ari.

Gerald makes a brief appearance, still recovering from his wound. He is out buying something when Ari carjacks him in order to draw Ducky out; he then holds Ducky temporarily and lets Gerald go. Gerald rushes back to headquarters to help them to find Ducky. (Ari didn't really want either of them.)

Director Morrow appears in only one scene to announce that he is moving on. He is going to be working in the Department of Homeland Security, and Jennifer Shepard will take over for him at NCIS. He also tells Gibbs that he has signed off on Kate's Presidential Medal of Freedom.

Special Agent Paula Cassidy comes on board to help with a case, and none of the team will allow her to sit in Kate's old desk. She tells Tony that Kate was a good agent.

Kate's name was in the Washington Post, and it was written that she was killed by a terrorist. The killer uses Kate's death to torture Gibbs a little.

Kate was in charge of inventory.

At the end of the episode, Ziva, who has quietly and respectfully moved into Kate's desk, gives Gibbs Kate's last sketchbook, which includes more drawings of everyone on the team. You can find them on Kate's profile page.

During McGee's conversation with Tony, he expresses a great amount of self-doubt in his abilities as a field agent. He cites his teammates as counterexamples to himself: Tony, Gibbs, Kate and her experience with the Secret Service, and finally Ziva.

At the end of the episode, Ziva, who has quietly and respectfully moved into Kate's desk, gives Gibbs Kate's last sketchbook, which includes more drawings of everyone on the team. You can find them on Kate's profile page.

Gibbs and several high school students are being held hostage by a teenage boy who insists on seeing his mother, who is "officially" dead. In order to alert Gibbs to that fact that the mother is dead (so they believe at the time), Tony tells the boy that Special Agent Caitlin Todd is out looking for his mother.

Gibbs has not recognized any of his team because of his amnesia; he only remembers hearing of his wife and his daughter's deaths. Ziva brings Gibbs back to the present by reminding him of Kate's death and, subsequently, Ziva's killing Ari.