Season 3 ended when a bomb exploded as Gibbs was contacting an undercover government agent on a suspicious foreign ship, killing the agent and placing Gibbs in a coma, in which he had flashbacks of the murder of his wife and daughter many years earlier, and his wounding in Desert Storm.
Meanwhile, Tony became the temporary head of the investigation team as the group attempted to track down Pinpin Pula, a missing crew member of the ship, suspected to be an Abu Sayyaf member.
Shepard contacted Gibbs' NCIS mentor and partner, Mike Franks, in the hopes of helping an amnesiac Gibbs regain his memory, as only he knew the details to the impending terrorist attack.
Ziva, who had appeared nonchalant about Gibbs' situation, visited Gibbs in a desperate and emotional attempt to revive his memory by telling him about their shared connection with Ari.
In her desperation in trying to help regain Gibbs' memory, she grabbed Gibbs' hand and used it to slap herself on the back of her head.
This, together with her emotional statement that she had killed her own brother for him, let Gibbs miraculously regain his memory. They both promptly returned to their headquarters, much to the surprise of the team.
In a live video conference, Washington bureaucrats ignored Gibbs' warnings about the impending terrorist attack on the naval vessel, because of a fear of negative publicity.
As a SEAL team arrived at the ship to find Pinpin Pula, the terrorist detonated the bomb and destroyed the ship while the NCIS watched on the large surveillance screen.
This prompted Gibbs to resign. He handed his badge to Tony, telling him that he was now in charge of the team and that he was ready for the responsibility.
The season ended with Gibbs arriving at Franks' house in Mexico, now in retirement.
In the first episode of Season 4, Ziva thinks about surrendering to the FBI after accidentally witnessing a political assassination. She is suspected by the FBI to be a double agent and has to deal with the consequences without Gibbs's help, who is now enjoying his retirement.
She decides against turning herself in and escapes while the NCIS team, led by Tony, must prove that she is innocent.
However, when things get more complicated, Ziva seeks help from the one person who always trusted her - Gibbs.
New characters introduced in this season are Michelle Lee, who was briefly on DiNozzo's team and was transferred to the legal department upon Gibbs' return, and (already in the final episodes of Season 3) Gibbs' former mentor Mike Franks.
Also, albeit later in the season, Hollis Mann is introduced as another love interest for Gibbs.