As a result of Emeron's continued refusal to join the Alliance Daleks in their "crusade against evil" because of their own "petty concerns," the Mentor ordered a plague unleashed upon the planet. When Mirana went to Kalendorf to discuss the situation with him, he obliquely warned her that the Mentor was likely listening to or watching their conversation. She told him an unidentified transmission has been detected coming from his flagship, the Courageous. The second wave of the Enemy Dalek fleet is in Venus' solar orbit.
Half of the Alliance fleet is taking shore leave on the terraformed Jupiter. Herrick has ordered that engineering teams begin to process the planet's mineral deposits. After Herrick loses contact with two perimetre guard patrols, he sends Sgt. Allenby and the 5th Airborne Division to investigate, but soon loses contact with them as well.
The Alliance gunship B68 is still making its way towards the Defiant, which still does not respond to hails. The Mentor has grown suspicious of the atypical lack of concern which Kalendorf has expressed for Mirana, leading her to the conclusion he is hiding something from her. She orders all updates of the B68's progress be communicated to her before being reported to Kalendorf. Furthermore, she orders a thorough investigation of Kalendorf's recent activity.
While reporting to Kalendorf, Comms Officer Sparks hears the sounds of gunfire and is soon killed by a creature which bursts from a shuttlecraft. After losing contact with Herrick, Kalendorf orders Jupiter evacuated, as they have clearly walked into a trap. At the orders of the Dalek Supreme, the Enemy Daleks have placed varga plants on the surface of the planet.
The Enemy Daleks used the brain analysis disc to resurrect the Dalek Emperor's consciousness. However, it was not a permanent process. Alby believes that the Dalek Emperor placed its consciousness in her mind as it knew that Suz would be the most likely of all the humans intended for robotisation to be rescued, given her friendship with Kalendorf, her status as the "Angel of Mercy" and Alby's love for her.
Mirana and Marber escape the Defiant in an escape pod and begin searching for Alby's ship. However, the pod runs out of power. Before they die of asphyxiation, Mirana tells Marber of the transmission she had detected, and her concern that Kalendorf may be planning to switch sides.
The Enemy Daleks have engineered the varga plants to not only transform its victims into brainless creatures, but to create a pack mentality for them to produce an army of psychotic killers.
The Mentor relieves Kalendorf of his command of the Alliance fleet and orders the Alliance Daleks bring him to her on Lopra Minor so he can undergo correction, their equivalent of the robotisation process. The hospital space station in the Pkowik system was built for that purpose. Kalendorf gave them to the coordinates. When the Courageous is boarded by the Varga men, Kalendorf makes his escape in a stolen shuttlecraft and sets course for the Defiant at maximum hypervelocity. The Mentor gives orders that he is to be neutralised if he resists.
As with all of the other patients on the station in the Pkowik station, Morli underwent correction at the hands of the Alliance Daleks, seemingly having been programmed to kill Suz if she ever had the opportunity. However, she is exterminated by the Enemy Daleks before she has a chance to do so.
The second wave of the Enemy Dalek fleet destroys the entire first wave of the Alliance fleet orbitting Jupiter. However, they are no match for the second wave of the Alliance fleet.
Using his telepathic abilities, Kalendorf informs Suz that he has forged an alliance with the Dalek Supreme to destroy the Mentor and the Alliance Daleks from the parallel universe. He intends to have Suz send a message, which the Enemy Daleks will relay across Mutter's Spiral, that the Angel of Mercy has returned, that the Enemy Daleks have made that possible and humanity must switch sides to defeat the Alliance Daleks.
- Susan Mendes - Sarah Mowat
- Alby Brook - Mark McDonnell
- Kalendorf - Gareth Thomas
- Mirana - Teresa Gallagher
- The Mentor - Hannah Smith
- Morli - Dannie Carr
- Siy Tarkov - Steven Elder
- Saloran Hardew - Karen Henson
- Scientist - Simon Bridge
- Herrick / Trooper / Varga Man - Jeremy James
- Allenby - Mark Donovan
- Sparks / Marber - Ian Brooker
- The Daleks / The Alliance Daleks / The Dalek Supreme - Nicholas Briggs
- 2,500 years later, Kalendorf is known as "The Dark One" and "The Bringer of Death" for bringing about the Great Catastrophe.
- The Mentor refers to Skaro as the home planet of the Enemy Daleks in the primary universe.
- All of Dalek War is told in retrospect.
- Although they are the three main characters in the series, this story marks the first and only time that Suz, Kalendorf and Alby are all together in the same place.
- The Enemy Daleks have placed varga plants on the surface of Jupiter. (TV: Mission to the Unknown, The Daleks' Master Plan) The Mentor tells Kalendorf that they originated on Skaro, the home planet of the Enemy Daleks. (TV: Mission to the Unknown; AUDIO: Purity)