When the War Doctor arrived on Gallifrey to show Rassilon and the High Council of a new Dalek plot to wipe Gallifrey from history, Karlax and the Castellan kidnapped the Doctor's companion, Cinder, and exposed her to a mind probe.
When the Doctor escaped his imprisonment on Gallifrey, Karlax pursued him with some help from the Celestial Intervention Agency. When the CIA and their Battle TARDISes were attacked by Dalek stealth ships, the Doctor materialised around Karlax and saved him from death, though he still had to regenerate. The Doctor and Cinder took Karlax to the TARDIS' Zero Room where he could recover.
After regenerating, Karlax regained consciousness and attempted to take the Doctor's TARDIS back to Gallfrey. The Doctor planned for Karlax's deception and set the TARDIS controls to make it dematerialise around the Doctor if Karlax tried to pilot it. Realising he had been tricked, Karlax tried to kill the Doctor, but Cinder pushed him out of the way and took the shot. Outraged by his actions, the Doctor dematerialised his TARDIS, setting the controls so that Karlax would be left behind in the middle of the Dalek Eternity Circle, who swiftly gunned him down. (PROSE: Engines of War)