On the way to the semi-finals, Noah Kaiba and the Big Five forced them to land in his water fortress, thus sending them to the digital world. After escaping the digital world, Gozaburo Kaiba tries to stop them from escaping the water fortress but is thwarted by Franz Hopper with the tsunami while the battle ship transforms into a jet. Team Lyoko find out that Gozaburo was possessed by XANA.
After the Battle City Finals, the duelists had to leave the blimp since it wasn't working and the island of which the final duels were held was going to self-destruct in less than 30 minutes.
The Kaiba Craft 3 was salvaged by Dr. Eggman, who turned it into the Eggman Craft 3 and deployed it against Sonic.
After XANA's defeat, Eggman said he would scrap the Eggman Craft 3 soon and Rouge had to make new living arrangements. It is unknown if he actually did.