At Kadic, Ulrich, Aelita, Odd, and Jeremie meet up in the courtyard in the morning. Just before breakfast, Hiroki approaches them and asks to speak with Ulrich privately. Hiroki then confesses to having feelings for Milly Solovieff, and asks for advice on how to get her to notice him. Ulrich suggests talking to her about her interests, namely journalism, and Hiroki interprets this suggestion to mean he should find her a story to put in the school paper. At breakfast, Ulrich, Odd, Aelita, and Jeremie discuss Hiroki's crush on Milly before Jeremie reveals he has developed a new program to search for William in the Digital Sea, and suggests they test it that afternoon.
A few moments later, when Yumi sets her backpack down to use a vending machine in the courtyard, Hiroki steals her diary from her bag, planning to find something revealing and newsworthy in it to show to Milly. Yumi catches her brother in the act and gives chase. While trying to escape his sister, Hiroki runs into Odd, who is walking with Ulrich nearby, before fleeing into the park. When Yumi finally catches him, it is then revealed that Hiroki accidentally dropped the diary when he ran into Odd and Ulrich.
Ulrich finds the dark-colored journal and begins to flip through the pages to figure out whose it is. In it, he comes across a photo of himself on the inside of one of the written pages. Briefly stunned, he realizes the book is Yumi's diary. Despite Odd's persuasions to read it in order to see what Yumi truly thinks of him, Ulrich resists the temptation to read the diary any further, firmly stating that whatever was written inside is none of his business. He then insists that it didn't matter since he and Yumi are just good friends, but Odd asks him, "Are you sure?" and Ulrich admits that he actually isn't sure at all.
After classes let out, Odd and Ulrich find Yumi in a sullen mood following the morning events. Ulrich attempts to give the diary back to Yumi. However, he is interrupted when Hiroki approaches her and apologizes to her for taking it in the first place and then losing it. When Yumi does not accept Hiroki's apology out of anger, Ulrich decides to make things right by rigging a system where everyone wins, realizing that if he had returned the diary like he was about to, Yumi would still be angry at Hiroki. Odd and Ulrich decide to hide the diary in the park so that Hiroki will find it and reconcile with his sister. However, when Hiroki finally locates the book in a pile of leaves, all of the pages have are missing, and only the cover remains. Things go from bad to worse when Yumi follows the boys to the park and sees Hiroki with her ruined diary. She becomes even angrier and vows that she will never forgive Hiroki for his actions (regardless of the oblivious circumstances). No one knows what to do since Odd claims it was all in one piece when he hid it.
That afternoon, the Lyoko Warriors go to the Factory, where Ulrich, Odd, Yumi, and Aelita are sent to Sector Five. After they all board the Skid, Aelita pilots the ship out of Lyoko and into the Digital Sea while Jeremie implements the new program. However, a problem occurs and a bug in Jeremie's program damages the Skid's sonar system. Without sonar, the mission is impossible and Aelita turns the Skid around to return to Lyoko. But on the way home, the skid is attacked by three Kongres, and Ulrich, Odd, and Yumi are released in their Nav Skids to fight them off.
Once the battle is over, Ulrich and Odd return to the Skid, but Yumi fails to return. After briefly wondering what could have happened to her, they deduce that Yumi could've been hit by a laser, which would only mean one thing: Odd asks if it were possible Yumi has been permanently devirtualized, but Jeremie goes over the stats from the battle, which reports no such result. With the Skid's sonar still damaged, the other Lyoko Warriors cannot search for Yumi until proper repairs have been made to the Skid by Jeremie and Aelita as they could end up lost at sea as well. Meanwhile, somewhere in the Digital Sea, Yumi is drifting aimlessly in her Nav Skid (which sustained a nasty dent from the battle) and trying in vain to contact Jeremie and the others while its power is rapidly draining.
As Jeremie and Aelita work to repair the Skid's sonar all the while trying to locate Yumi on the Network, Ulrich and Odd go back to the park. As Odd calms Ulrich's fears about what could have happened to Yumi, he discovers the pages of Yumi's diary had been stolen by Kiwi. Odd realizes that Kiwi had taken the pages and buried them in a separate area away from the cover as a result of believing that he was playing a game with them. Ulrich takes the pages from the dog as he continues to worry about Yumi. Back in the Digital Sea, the power in Yumi's Nav Skid is almost completely exhausted and she is approached by another Kongre. She tries to blow it up with her single-remaining torpedo, but cannot as she does not have enough power to fire it. However, she gains the power when she diverts energy from her defensive shield and manages to destroy it with her last torpedo. The explosion is detected by Jeremie and Aelita in the lab, who recognize it as a sign that Yumi is still alive. Aelita calls Ulrich and Odd back to the Factory as Jeremie triangulates Yumi's location from the explosion. Even though Yumi is still alive, she's still afraid and alone in her Nav Skid with no way to contact Jeremie, all the while reminiscing about all the fun times she spent with Hiroki over the years, regretting the anger she showed him earlier that day.
Back in the Factory, Jeremie has finally localized Yumi just as everyone arrives. He speculates that she got sucked down a hub during the battle with those first three Kongres, which would explain why he lost all trace of her. Despite the Skid's sonar still in need of repairs, Ulrich, Odd, and Aelita all volunteer to go on a rescue mission, and the three of them return to the Digital Sea. They set sail and find the hub Yumi was sucked into, which will beam them straight to her position.
Meanwhile, Yumi is attacked by yet another Kongre. Now defenseless and out of ammo, Yumi is forced to flee, navigating through the internet until she loses control and crashes it into the buildings above. With her propulsion systems completely disabled, Yumi is now at the mercy of the Kongre and she resigns herself to death, but the monster does nothing and decides to flee. Yumi is confused until she sees William in a specially made submarine of his own coming straight for her. Things appear hopeless when William fires at Yumi, but she is defended by the Skidbladnir, which arrives at her side just in time to block the attack. Yumi anchors herself to the Skid while Odd and Ulrich battle both the Kongre and William. Ulrich destroys William's submarine and him along with it, and the newly reunited group returns to Lyoko together. As they return, Aelita silently vows that one day, they will rescue William.
That night, after returning to Earth, Yumi enters her bedroom to find the pages of her diary lying on her bed. Hiroki then appears in her doorway and apologizes again for stealing it. Yumi, sobered by her experience on the Network, forgives him. It is then revealed that Ulrich secretly placed the pages in her room by climbing a tree into her house. After seeing the siblings make up, he walks away from the Ishiyama residence while humming and smiling to himself in victory.
- The original French name of this episode is Torpilles virtuelles, which translates to Virtual Torpedoes in English.
- William's personal submarine, the Rorkal, is introduced in this episode.
- When Odd and Ulrich step into two of the scanners, Aelita steps into the third one, but is not virtualized with Odd and Ulrich for some reason.