Jeremy and Aelita are doing all they can to find out more about Tyron, but all they can find is that he had disappeared on June 25, 2003. After creating false security codes, they all go to the lab; all save Ulrich who is hurt becasue of an essay Yumi had written earlier which had been referring to him and unreliable attitude. This bothers Yumi and has a Ninja devirtualize her so she can talk to Ulrich.
After devirtualizing several Ninjas with ease, William, Odd and Aelita return to the Skid; unaware that an additional Ninja is hot on their trail. Jeremy unlocks the code and finds Tyron's location in Switzerland, but a disturbing sigh appears after he cracks the encryption. On Lyoko, the Ninja reveals himself and devirtualizes Odd, Aelita and William quickly. Jeremy calls Ulrich, who comes and uses his triplicate ability to devirtualize the Nina. But not before he places a metallic beacon underneath the platform, which begins ticking ominously.
The next morning, Yumi and a friend are handing out flyers to local students at the school entrance. It soon becomes apparent that Ulrich was supposed to help out as well, but has clearly forgotten about it. In the spur of the moment anger, Yumi writes all of her unfriendly feelings down in the form of an essay paper for a class assignment, not intending for anyone to read it.
However, when the group meets up for mission planning, William tells everyone how Yumi received a 110% on her paper. Shocked since no student has ever received a score higher than 85% in the class, Odd sees that Yumi has the actual paper in her hands and grabs it. Despite Yumi's protests for him to give it back, Odd proceeds to read it aloud for the group to hear. The story turns out to be about a girl named Mia whose long-term friend and soul mate named Eric suddenly "unveiled another face". He does not actually care about anyone, the terms "immature" and "stubborn" being used to describe him, ultimately resulting in the break up of the two's friendship. Everyone (except Odd and William) hears the double meaning in Yumi's paper, especially Ulrich who seems to instantly see that Yumi is actually talking about him and is obviously hurt.
On the way to the Factory for the mission, a hurt Ulrich confronts Yumi about the paper, wanting it to be confirmed that she was talking about him. Yumi tries to insist it was only an essay assignment for a class, but Ulrich can clearly see it was actually about him. He remains upset about her harsh words towards him and she says they can just talk about it after the mission. However, Ulrich refuses. He abruptly suggests that they spend some time apart for the time being, remarking that it seems to be for the best. He tells her how he has always been honest with her before leaving, humiliated. Yumi silently watches as he walks away.
The rest of the group go over the plan for Jeremie's new program as she returns, obviously upset and not wanting to discuss Ulrich's absence. They are all transferred to Lyoko and arrive on the Skid to do the usual trip to the Cortex and the usual MegaPod ride to the Core of the Cortex. Along the way, Yumi is clearly guilt ridden about her nasty words aimed at Ulrich early on. Meanwhile, Jeremie tries to call Ulrich, wanting an explanation for his sudden absence on the misson. However, Ulrich, who is lying on his bed in his room deeply depressed, ignores the call.
The group on Lyoko soon arrive to the Cortex and insert the information card into the interface. They begin to fight off a group of Ninjas and easily avoid any blows. However, Yumi demands during a fight with Ninja that Jeremie devirtualize her. Jeremie refuses her abrupt request since she is needed to protect Aelita. Yumi then allows the Ninja to devirtualize her, leaving Odd and William to take care of the remaining Ninjas. Jeremie, confused about Yumi's sudden abandonment of the mission, watches from a camera as Yumi immediately races out of a Scanner and straight out of the Factory.
In the virtual world, things are going fine until traps suddenly become activated, forcing Aelita, Odd and William to flee in the MegaPod with a single Ninja right on their tail. Yumi, meanwhile, returns to Kadic to check up on Ulrich, asking a fellow student where he is at. She learns that he is in his room and she goes off to see him.
The team are leaving in the MegaPod as a Ninja decides to use its incredible stealth abilities to follow them, but the stealth appears to wear off for a moment, leaving the Ninja momentarily weak. The group then quickly come back to attack him right when he appears to have fled. Assuming the Ninja has left, they get on the Skid and return to Lyoko with the Ninja still on their tail. During this, Yumi has come to Ulrich's dorm wanting to make amends with him. She repeatedly knocks on the door, but he refuses to open it. She gives a sincere heartfelt apology to him and admits that the guy in her paper was, indeed, about him. She eventually gives up and leaves, seconds before Ulrich opens the door to watch her walk away. The team, back in the virtual world, are teleported back onto the Skid and begin travelling back to Lyoko, unknowingly, with the Ninja (literally) right on the Skid.
As Yumi walks back to the Factory through the forest, Ulrich quickly catches up with her. He is still upset about what she said about him, annoying Yumi that out of all the good things she had written about him, he can only remember the negative. Yumi tells him to "grow up" and directly tells him that he actually means a lot to her, also confessing she couldn't stop thinking about him while on the group mission. She walks off in a huff, causing Ulrich to trip when trying to follow after her. This causes Yumi to smile in amusement. Ulrich apologizes to her and admits she is right about him. He tells her that she is the most important person in his life and he doesn't want to lose her, promising he will make an effort from now on. Yumi says the same goes for her about him and they smile at each other, clearly having a moment.
Meanwhile, upon teleporting out of the Skid, the ninja reveals himself and easily devirtualizes Aelita. Odd attempts to eliminate it, only to be devirtualized himself. Realizing the drastic down turn for the mission, Jeremie calls Ulrich yet again and informs him of the situation at hand in Lyoko. Ulrich and Yumi then quickly head for the factory. William is seemingly on par with the ninja due to his Supersmoke ability, but is quickly knocked aside as the ninja runs off in another direction. William follows after him just as Ulrich arrives to be virtualized.
Ulrich arrives just in time to see William defeated when the ninja grabs him by the arm, therefore preventing him from swinging, and slicing into him with his sword. Ulrich begins to battle the ninja and uses his triplication ability to confuse the ninja. He knocks the ninja down only for him to hold onto the edge with one hand. Ulrich easily shoves him down, unaware that the ninja placed what appears to be a tracking device on the underside of the walkway to the Skidbladnir's elevator.
- When Aelita, Odd, and William are being transferred back to the Skid, Yumi is also shown to be teleported as well, despite being devirtualized earlier.
- Ninjas are shown to have two unique abilities: they can activate an ability similar to Ulrich's Super-sprint, and they can also apparently withstand the harsh currents of the Digital Sea without negative consequences.
- Ninjas are seen in Carthage and the outside of the Cortex for the first time.
- Ulrich uses Triplicate for the first time in Season 5.
- Odd, William and Ulrich manage to devirtualize a Ninja for the first time.
- This marks the first time one of the Ninjas has entered the Digital Sea.
- Ulrich and Yumi finally admit how much they truly care about each other and rekindle their relationship.
- This is the first time there was a stowaway on the Skid.
- A Lyoko Warrior jumps down the elevator access without taking the elevator for the first time.