While Ben is trapped in Khyber's ship, Khyber tells Ben that he needs different alien DNA to complete the evil incomplete version of the Omnitrix the Nemetrix he also reveals that Dr. Psychobos assigned him to hunt down various species for DNA to transfer it to the Nemetrix and also tells Ben that the reason Dr. Psychobos is creating an evil Omnitrix is because of the orders from Malware. After Ben breaks free, a brawl breaks out leaving Khyber the victor.

Just when it seems Ben is finished, Rook breaks in and saves Ben the duo then reveals to Khyber that they orchestrated the whole "fight" at Undertown and Ben only let Khyber capture him so he can lead them to his ship. After a long fight Ben and Rook accidentally crash Khyber's ship eliminating the DNA to complete the Nemetrix, Khyber and his Dog emerge unharmed as Malware and Dr. Psychobos arrive.