Jeremy decides to teach Odd, Ulrich, and Yumi how to use the Supercomputer in case he or Aelita are unable to, being X.A.N.A.'s favorite targets. During the lesson, Jeremy is attacked by one of X.A.N.A.'s polymorphic clones, leaving the others to operate the Supercomputer without help. Aelita is at the final audition with the Subdigitals, competing against two other candidates, and thus cannot be contacted. To make matters worse, the clone heads for her after dealing with Jeremy. Using what they learned from Jeremy, the others are able to rescue Aelita and deactivate the tower without his help. Aelita is also chosen as the winner of the audition despite her walking out on them.
Sanjay has a new experience. Nancy gets bruised. Conrad won't do what U-Turn wants him to. Lupita still won't follow orders. Heylia's out to handle a few things. The Amber Alert is still out on Shane. Andy gets in trouble with a couple who make him for a child molester. Silas gets to talk to Shane. Celia is still having problems with her husband and daughter. Doug begs Celia to forgive him.
Tom has trouble focusing on the hunt for Richard Tyler because of dreams he's having about the future.
Science-fiction addict Kevin believes aliens from outer space may have landed. Truly, Clegg and Alvin help to convince him he is right.
Barb finds out that her mother is about to re-marry. Bill hears disturbing news about Weber Gaming. Meanwhile, Nicki is upset by outside influences on her children.
While on a trip to visit Bruce, Johnny views a racehorse being stolen in a vision. He also realizes that he may have lost the chance to reunite with Sarah and J.J. thanks to Stilson's efforts.
To try and re-invigorate his marriage, Brett decides a romantic trip away to tropical Queensland could be just what is needed. Elsewhere, Kath is feeling flat and Sharon is accused of the greatest sporting crime of all.
A performance at a local "World Music Jam" results in the Conchords gaining two new fans, but Mel is suspicious of the newcomers and their motives. Murray encourages the band to adopt a more "rock star" attitude.
Filmmaker Skull Boy sets out to bring his script, `The Adventures of Skull Kid' to the big screen! However, it turns into a wacky cartoon based on Ruby and friends...to mixed reviews.
Vince, Ari, and Dana Gordon receive the script for Vince's next project, but Billy's interpretation is vastly different than what he was supposed to write. Vince loves the script anyway leading Ari to try and keep the studio interested. Eric is occupied with a new client and her boyfriend.
Doombots invade the Baxter Building in the middle of the night, but their attack is just a distraction for Doom to launch the Baxter Building into space.
Yeah, Kenichi’s a total wimp. He’s always getting picked on and doesn’t have a lot of friends to stick up for him. The guy needs motivation if he hopes to graduate in one piece. Well, Miu’s the perfect motivation. She’s hot, she accepts him, and she just so happens to live at a dojo with six martial arts masters. You could say fate has led Kenichi to their door, or you could say he was just following the hottie. Either way, he’s about to get whipped into serious shape. If he can survive some hard-core training, he might survive another day at school. He might even score with Miu. Yeah, you could call Kenichi a wimp. But let’s go with underdog instead.
Monk finds himself in a dangerous situation when he helps his psychiatrist's son follow a treasure map.
A Neuro causes the team to become stuck in a timeloop, causing them to relive the same day repeatedly. Meanwhile, the Neuro who caused the timeloop tries to finish an assassination.
A police dispatcher sees the spirits of a man and two women in her home and learns from a Bible-toting paranormal investigator that the male ghost is there to feed off her fear.
While their mother is out shopping, the boys build a roller coaster. Dr. Doofenshmirtz and Perry battle due to the doctor's evil plan of throwing the earth off its rotation.
Shawn and Gus are put on the case when a food critic is murdered. However, Gus' Uncle Burton is in town, and due to a misunderstanding, Gus must pretend to be the psychic detective to avoid disappointing his family.
Miley is envious of her Dad spending time jamming with the Jonas Brothers. Jackson tries to break the World Pogo-stick record.
The gang manages to convince Jeremy to let them test out the Skid. During this test, the navigation system bugs up, leaving the gang stranded in the digital sea. Jeremy runs to his room to fetch the backup programs, but forgets that it's Fire Safety Day and runs into several teachers, eventually having to scale the roof to get to his room. Meanwhile, the Skid stumbles upon another Lyoko and is attacked by two eel-like monsters. Jeremy is able to repair the navigation system and bring his friends home, after which he surmises that the replica of Lyoko is created from the portion of the Keys to Lyoko that X.A.N.A. has stolen from Aelita's subconscious in the second season finale, The Key. Jeremy wonders how he plans to use it.
The new virtual, submersible "submarine" (as Jeremy calls it) is almost complete, the last step being a secondary program that needs to be run by 4 PM the next day. However, when Aelita and Jeremy stay up late to set the program up, they are caught and given detention. Meanwhile, William takes the opportunity to attack the incomplete ship, forcing Yumi to run the Supercomputer in Jeremy's absence. Odd and Ulrich are unable to handle the situation, but Jeremy and Aelita are able to sneak out in time to help. Aelita is able to repel William with a massive attack, allowing Jeremy to complete the sub on time. It is later christened the Skidbladnir, nicknamed "the Skid" by Odd, after the Norse ship.