- "It's not the danger. It's the fun."
- —Cole to Gibbs in the Season 9 finale episode, "Till Death Do Us Part".
Jonathan Cole, a former U.S. Army Special Forces operator, was a member of the special operations team with callsign "Phantom Eight". He conducted multiple operations with Phantom Eight, but ultimately turned rogue under orders from his commanding officer, Sean Latham. He is the main antagonist of Season Nine; his primary target is Special Agent Erica Jane Barrett.
He later helped NCIS in tracking down Harper Dearing and attempted to defuse a bomb planted in the Navy Yard, but the bomb was set off before he could defuse it, killing him in the process while causing great damage to the Navy Yard as well as claiming numerous victims.
His prior life before joining the U.S. Army is unknown. At some point, he completed Special Forces training and received his green beret, before being recruited into Phantom Eight under Sean Latham along with Gayne Levin, Felix Wright, and four other operators. He eventually went rogue, along with his CO, Latham. The two killed or stole microchips from several of their former comrades; these microchips served as skeleton keys for any electronic locks in the world. They sold them on the black market to international bidders.
However, Special Agents Simon Cade, Anthony DiNozzo, and Erica Jane Barrett are investigating the suspicious circumstances; Barrett had retrieved Levin's chip upon his death, DiNozzo was assigned to kill Cade, who was believed by the Navy and SECNAV Clayton Jarvis to have been responsible for stealing the chips, and Cade had been caught in the middle.
As a result, Cole was ordered to murder the three. He arranged a meeting between the three, making it appear as though each had invited the others. When the three Special Agents met, Cole ambushed the trio, killing Cade. However, EJ was able to escape when her body armor stopped the bullet, while Tony appeared to be dead when he collapsed and struck his head, falling unconscious. He was able to retrieve Levin's chip and gave it to Sean Latham who sold it on the black market to international bidders.
He also switched the ammo of DiNozzo's gun and planted the blood-stained badge on him so that, in case he survived, DiNozzo would have been framed for killing an NCIS agent in cold blood, having known about DiNozzo's secret mission to kill Cade for stealing tracking chips and selling them onto the black market.
In addition, he also disguised himself as Special Agent Casey Stratton of the FBI so that he could finish the job of killing DiNozzo. However, he was forced to abandon the plan when he saw that a psychologist was also in the room. The brief glimpse of "Stratton" also allowed DiNozzo to remember that he was the one who shot them, although further investigation led them to lead to a dead end when the FBI revealed that "Stratton" never actually existed. He then returns to the Watcher hideout where he and Latham start the bidding process of the Phantom Eight chips (with countries such as Korea and various Arab states acting as the bidders).
Cole then tracked EJ for the better part of a year, finally tracking her down in New Jersey. He hired Captain Dane Marseilles, a former Navy SEAL, to murder EJ, who had taken refuge with a Naval Officer she had befriended while in Spain. The assassin killed the officer with a Beretta M9, but failed to kill EJ, who again escaped when her body armor stopped the bullet. Cole, enraged at the SEAL's failure, murdered him and left his corpse for NCIS to find.
At this point, Gibbs made the connection between Cole and Latham, and interrogated Latham. Latham meets with Cole in a park and warned Cole to leave the country, after giving him the safehouse location where he believed EJ and Tony were staying. Cole refused to leave, and murdered Latham, before going after EJ and Tony. He destroyed the safehouse with an RPG, but was captured by the FBI and Gibbs, McGee, and Ziva after a gunfight. It was revealed that he had again failed to kill his targets; Latham had been given the wrong safehouse location.
After being taken into custody, he defends the Phantom Eight program and his role in it, he also reveals that he knows that Gibbs murdered Pedro Hernandez in Mexico, decades ago, as a warning to Gibbs that if he was sent to prison, Gibbs would hang beside him. As of yet, his fate has not been revealed.
It has also been implied that, thanks to his and Sean Latham's earlier auctioning of the Watcher microchips, he was also indirectly responsible for the theft of the Aquamarine documents as well as the death of fellow Phantom Eight member Carter Plimpton and the current arson-terrorism against the United States fleet.
Cole returns in the Season 9 finale episode, Till Death Do Us Part (episode). He is first seen being brought into NCIS much to Tony, Ziva, McGee, and Palmer's shock, as he smiles at them. He was apparently the one who had sold Harper Dearing the Watcher Fleet microchip helping Dearing with the terrorist attacks on U.S. navy ships. He turned double-agent and helped NCIS with tracking down Dearing, by being released from prison and putting the tri-state area on high alert, grabbing Dearing's attention.
Dearing set up a meeting with Cole, but did not meet him in person; rather, he dropped off a cell phone to relay a message to Gibbs. Gibbs' team tracked down Dearing's location using the call, and realized that Dearing was nearby and soon came to the conclusion that he had planted a bomb on Vance's car. Cole was an expert at bomb disposal, so he offered his help to Gibbs to attempt to defuse the bomb.
After searching Vance's car, Gibbs and Cole finally located the bomb, which was wired to a cell phone. Gibbs offered Cole his army knife and ran back to evacuate Abby, and Cole prepared to defuse the bomb, but at that moment, Dearing made the call, exploding the bomb and killing Cole in the process.
- Captain Felix Wright- (shot dead).
- Special Agent Simon Cade- (shot dead).
- Captain Dane Marcelles- (stabbed and thrown off high story building).
- Sean Latham- (stabbed).
- James Barnesway- (shot by Dane Marcellus).
- Carter Plimpton- (was killed by Harper Dearing via arsonist-for-hire Bruce Johnson to get the Project Aquamarine file, which Dearing knew about thanks to his receiving the Gavin Levine watcher microchip that he and Latham auctioned online).