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. It soon becomes apparent that Ulrich was supposed to help out as well, but has clearly forgotten about it. In a spur of the moment anger, Yumi writes all of her unfriendly feelings down in the form of an essay paper, 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, shocking everyone since no one ever had received higher than 85% in the class. Odd sees Yumi has the paper in her hands and grabs it to read it out loud for the whole group to hear. Despite Yumi's protests for him not to, Odd reads it aloud. The story turns out to be about a girl named Mia whose long-term friend and soul mate named Eric "unveiled another face" and actually doesn't care about anyone, the terms "immature" and "stubborn" being used to describe him, resulting in the break up of the two's friendship. Everyone 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, in fact, about him. He remains hurt about her harsh words towards him and then suggests they spend some time apart for the time being and leaves, refusing to attend the mission with the group, 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 about Ulrich early on. Meanwhile, Jeremie tries to call Ulrich, wanting an explanation for his sudden absence on the misson, but Ulrich, while lying on his bed in his room, ignoring the call.
The group on Lyoko soon arrive to the Cortex and insert the information card into the interface. They begin to fight off some Ninjas and easily avoid any blows, but Yumi suddenly demands during a fight with Ninja that Jeremie should devirtualize her. Jeremie refuses to since she is needed there 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 abrupt 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 still 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. At first, they begin to argue when Ulrich still remains upset about what she has 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, and walks off. Ulrich then trips when trying to follow after her, managing to get Yumi to smile in amusement. Ulrich apologizes to her and admits that she is the most important person in his life and he doesn't want to lose her. 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.