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 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 temptation to read the diary any further, firmly stating that whatever was written inside the diary 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. He attempts to give the diary back to Yumi. However, he is interrupted when Hiroki approaches her and apologizes to her for losing the diary. When Yumi does not accept Hiroki's apology out of anger, Ulrich and Odd 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 fallen out, and only the cover remains. Yumi discovers Hiroki with her ruined diary and becomes even angrier, vowing that she will never forgive Hiroki about the diary.
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 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. However, before the Skid reaches its destination, it 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 was hit by a laser and knocked into a Hub, sending her to another unknown part of the internet. 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. Meanwhile, somewhere in the Digital Sea, Yumi tries in vein to contact Jeremie and the others in her severely damaged Nav Skid. She looks back on her relationship with Hiroki, and regrets the anger she showed him earlier that day.
As Jeremie and Aelita work to locate Yumi on the Network, Ulrich and Odd go 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 when believing that that he was playing a game with them. Ulrich takes the pages from the dog as he continues to worry about Yumi. In the Digital Sea, Yumi is approached by another Kongre, 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 Yumi is still alive. Aelita calls Ulrich and Odd back to the Factory as Jeremie triangulates Yumi's location. Despite the Skid's sonar still being damaged, Ulrich, Odd, and Aelita all volunteer to go on a rescue mission, and the three of them return to the Digital Sea.
Meanwhile, Yumi is attacked by yet another Kongre. Now defenseless, Yumi is forced to flee, navigating through the internet until William arrives at her position in a specially made submarine of his own. However, when William fires at Yumi, she is defended by the Skidbladnir, which arrives at her side just in time. Yumi anchors herself to the Skid while Odd and Ulrich battle both the Kongre and William. Ulrich destroys William's submarine, and the newly reunited group returns to Lyoko together.
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 the diary, and Yumi, sobered by her experience on the Network, forgives him. It is then revealed that Ulrich secretly placed the pages in her room, climbing a tree into her house to do so. After seeing the siblings make up, he walks away from the Ishiyama residence while humming and smiling to himself.
- The original French name of this episode is Torpilles virtuelles, which translates to Virtual Torpedoes in English.
- Because of the characters wearing their Seasons 1-3 attires in the previous episode, Lost at Sea marks the return of their current outfits since the events of Hot Shower.
- 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.