The Phantom Ninja is a major character that appeared in Cole: Ninja of Earth. He is a skilled ninja that wears a charcoal gray suit - although associated with Sensei Wu, he works independently.
After the Ninja failed to work as a team, Kai began an argument about Cole's leadership. Jay agreed that they should consider a different leader altogether, suggesting himself as a likely candidate. Cole, however, retorted with the fact that leadership would be too difficult for any of the three, leaving his comrades to think it over. Zane thought they should go fetch Cole, but Kai interrupted him to decide a new means of choosing the next leader: whoever performs the best in the next mission will be leader.
The next morning, the Ninja found that Cole was missing along with their equipment. The three quickly searched for the Earth Ninja, only to find him unconscious in a field of grass. With the splash of cold water, Cole awoke from his forced slumber, complaining of a headache and claiming that something wiped him out while he was guarding their campsite. While they debated about the cause, Kai found a note attached to a tree held up by a single shuriken. The note was signed by the Phantom Ninja, admitting to being the one who stole their possessions and warning that he would take something more precious if the Ninja did not surrender.
Cole then told his team a story about Sensei Wu attempting to recruit the Phantom Ninja, but changed his mind when the Ninja demanded gold in return for his services. The Phantom Ninja was not able to handle Sensei Wu's second thought, vowing to seek revenge. The Ninja turned to Cole for a plan to tackle the task, but Cole pointed out that he was no longer the leader, causing the three other Ninja to walk away in order to help themselves.
The Ninja agreed to a plan sorted out by Kai, though the trap they laid out failed to lure the Phantom Ninja. However, after they heard the shocked screams of Cole, the three Ninja went to investigate and found that the Earth Ninja was missing. A note rested in his place where his black ninja hood had been left behind, signed once more by the Phantom Ninja. It spoke of how he took Cole, warning that they will never see him again if they cannot find him by the next day.
They headed out through the forest in search of their missing friend. The three Ninja came across a broken bridge above a river, finding yet another note, which informed them that they must make it past the river without the use of Spinjitzu. Jay spotted some of his stolen gear nearby, creating a rocket pack and tying a rope around himself and his comrades. They flew across with success and crash-landed onto the other side of the river.
A single arrow shot past Zane with another note, though Kai ordered everyone to search for the Phantom Ninja instead as the arrow would indicate that he was close. In their chase, they became so focused they accidentally sprung traps that left them hanging upside-down by vines. The Phantom Ninja finally showed himself, laughing and taunting the group. He then gave them a clue of Cole's situation: Where is a man who is drowning, yet not wet? The Phantom Ninja vanished after his question, the Ninja quickly realizing that Cole must be in the quicksand nearby.
Zane, Jay, and Kai arrived at the pool of quicksand, spotting a black-garbed figure in the middle. Kai made a lasso out of some vines, though Cole made no effort to grab it and instead lay motionless. Zane and Kai turned to leave, Jay astonished with them as they left him behind. An axe was propelled at the ground where they were walking, the Phantom Ninja standing atop a branch above them. The Phantom Ninja questioned their actions, Kai telling the figure of the dummy that was placed in the quicksand, and Zane elaborating with details of his plan. Having been figured out, the Phantom Ninja pulled off his hood to reveal himself to be Cole.
Cole explained how he planned out the entire ordeal to teach the team a lesson about leadership, and when Kai asked him if he made up the Phantom Ninja, Cole admitted that the story was true.
The Earth Ninja informed his team that he returned their possessions to the campsite after they left, though when they headed back home, the campsite was completely trashed. At first the three Ninja assumed that Cole was lying about returning their luggage, but Cole was just as stunned as they were. The Phantom Ninja appeared before them, stating it was his doing before throwing shurikens at Jay. Cole demanded to know his reason for trashing their camp, though the Phantom Ninja replied that he heard his name was being used in vain. After Kai and the Phantom Ninja exchanged taunts, they both sprung into battle. He quickly paralyzed Kai with a sparrow strike, moving onto Zane next. The Phantom Ninja complimented Zane for his skill, though he took down the Ice Ninja with ease. Cole then sprung into action with Jay, using their Spinjitzu - however, the Phantom Ninja whirled around into a tornado of Spinjitzu and countered their attack. The Phantom Ninja disappeared afterward, Cole ordering his teammates to grab makeshift weapons using rocks and sticks. The gray Ninja reappeared moments later, Zane questioning how he performed such a technique. He explained that he simply emptied his mind of all thought, commenting that the technique should be easy for them.
Cole began to notice his comrades were becoming exhausted, coming up with a plan in an attempt to stop the endless battle. He ordered the Ninja to close in on their opponent and, once they were close enough, performed Spinjitzu which whipped the Phantom Ninja into the air. Once the gray Ninja fell, the Phantom Ninja began laughing before stating that he lost his wager. Confused, Cole asked him what he meant, the Phantom Ninja explaining that he and Sensei Wu participated in a bet to see if the team became too fractured to operate properly in a crisis.
Kai was baffled by his explanation, the Phantom Ninja elaborating further - the story that Sensei Wu told was made up. The Phantom Ninja was previously a bandit, and when Sensei Wu found him, they worked out a deal: Sensei Wu would not report him to the police if the Phantom Ninja only stole from other bandits and passed any information of major threats to Sensei Wu. Then he explained to them that he provided the team a common enemy when they needed it most, to bring them together.
Zane pointed out how after the entire ordeal, he was unsure of how he could just simply let him go back to his banditry. The Phantom Ninja said to the Ninja of Ice that it was just how things were, giving them the option of attempting to beat him again. Cole was forced to stop an infuriated Kai from attacking the gray Ninja, instead letting him off on the note of being ready for another attack if necessary. With that, the Phantom Ninja bowed, saying that he would leave Sensei Wu the tea in the "usual spot" and informed them where he placed their gear before vanishing.