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 in 2003 where Cole worked under Sean Latham along with Gayne Levin, Felix Wright, and four other operators.
Cole eventually went rogue, along with Latham as the two killed their former comrades before stealing and selling the stolen microchips taken from the bodies to international bidders with the chips being skeleton keys capable of unlocking any electronic lock in the entire world.
NCIS Season 9
At some point, presumably after the Port-to-Port killing case had been solved, Latham, friends with newly appointed SECNAV Clayton Jarvis leaked information stating that Special Agent Simon Cade was a traitor while Erica Jane Barrett secretly began investigating herself, having removed the microchip from Lavin's arm after Lavin had died after being shot by the killer, Lt. Jonas Cobb.
Jarvis took matters into his own hands and tasked NCIS Special Agent Anthony DiNozzo with capturing or killing Cade while Latham used the events to his advantage and tasked Cole with killing the three NCIS agents.
Cole responded by hacking the phones in question and luring all three to an alleyway for a meeting.
When they all got there, Cole struck, his shots injuring DiNozzo who hit the ground and was left unconscious by the fall while Cade wasn't so fortunate and died instantly after being shot with Barrett being the only one of the three to survive thanks to the bullet-proof vest she had been wearing.
In the aftermath, Cole retrieved Latin's chip and later gave it to Latham who sold it to some international bidders on the black market. Cole then switched the ammo of DiNozzo's gun and planted Cade's blood-stained badge on DiNozzo's body to make it look like DiNozzo had killed Cade in cold blood, Cole having known all along of DiNozzo's supposedly secret mission to find and kill Cade for stealing the tracking chips and selling them on the black market.
Knowing that DiNozzo had survived, Cole disguised himself as an FBI Special Agent named Casey Stratton so that he could use the fake identity to sneak into the hospital and kill DiNozzo. Unfortunately, the plan hit a snag when he saw that DiNozzo's boss, NCIS Special Agent Leroy Jethro Gibbs and psychologist Rachel Cranston were in attendance.
DiNozzo's brief glimpse of Cole/Stratton allowed DiNozzo to regain his memory where he finally revealed that Stratton had been the one who had shot at himself, Cade and EJ with the investigation hitting a dead end when the FBI revealed that they had no such agent known as "Stratton" working for them.
Hours later, Cole returned to the Watcher hideout where he and Latham started the bidding process of the Phantom Eight chips (with countries such as Korea and various Arab states acting as the bidders).
Cole then spent a year tracking EJ and finally chased her down to New Jersey where he tasked a former Navy SEAL, Captain Dane Marseilles with killing EJ for good but Marseilles failed due to the fact that EJ's body armor had stopped Marseilles's bullet from hitting her.
Enraged at the failure, Cole used Marseilles's phone signal to get NCIS's attention before he stabbed the SEAL to death. Cole then threw Marseilles's body out of his apartment where it landed on the ground below and knowing that NCIS would arrive, Cole fled, hiding in the background where he saw Gibbs and Agents Ziva David and Timothy McGee arrive at the scene.
Gibbs later realized that Cole and Latham were working together and confronted Jarvis with the hard-hitting evidence which left Jarvis stunned. The next morning, with Gibbs in attendance, Jarvis and Latham held a meeting where Latham revealed the truth about Cole to the men with Jarvis ordering Latham to bring Cole in.
A while later in a local park, Cole and Latham met with Latham telling Cole of what was going on before ordering Cole to leave the country. Cole refused and responded by stabbing Latham, fatally wounding the other man before Cole left to walk a dog while leaving Latham to bleed to death on a park bench.
The next day, Cole went to destroy the safehouse that he believed EJ and Tony were hiding in and succeeded although he got into a fierce gunfight with Gibbs, McGee and Ziva who had descended on the park to confront Code once and for all. Code attempted to flee, only to walk straight into a trap that NCIS had arranged for him with the FBI assisting them, presumably due to the FBI's anger over Cole pretending to be one of their agents.
It was also revealed that Jarvis had given Latham the wrong safehouse location and as such, Tony and EJ were spared while Cole was later cuffed and taken back to NCIS where during an interrogation, he defended the Phantom Eight program along with his role before revealing that he knew that of Gibbs's direct involvement in the murder of drug dealer Pedro Hernandez nearly twenty years ago while stating that if he was sent to prison, then Gibbs would hang beside him with Cole's own fate not being revealed.
As NCIS recovered from the disastrous fallout, they soon learnt that Cole 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 returned in the Season 9 finale episode, Till Death Do Us Part (episode). He was first seen being brought into NCIS much to Tony, Ziva, McGee, and Palmer's shock, as he smiled 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.
- "It's not the danger. It's the fun."
- —Cole's final words to Gibbs.
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, causing the bomb to go off and killing Cole in the process while severely damaging the buildings in the NCIS Navy Yard.
- 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 Barnsway- (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).