The Doctor and Ace arrive in England 1963 and immediately their services are called upon to deal with a Dalek in a barn. The local army are unable to deal with the threat so The Doctor uses bombs that he had bought with him.
The Doctor tells Ace that the Daleks are probably after the 'Hand of Omega' which is located nearby which he had left there on the last visit to the area. They venture to a school and down into its cellar where they discover a transporter. As a Dalek materialises, The Doctor causes the machine to malfunction and the Dalek is lost. As the maintenance Dalek arrives, they attempt to escape, Ace makes it out but the Doctor is faced with certain death as he's trapped by the school headmaster. After escaping The Daleks with a little help from Ace who recovers from her attack, they go outside, get a bazooka off the soldier and return to destroy the Dalek. The rest of the soldiers appear then they all leave. The Doctor visits the Hand of Omega and takes it away to get it buried.
The Doctor is called to Army headquarters where the Doctor explains the situation to the army and advises them where to look for the enemy. Ace who had been told to stay behind disobeys and goes to the school where the Daleks are massing. She's spotted and after a chase through the school, she is cornered in the car park. After rescuing Ace from the Daleks, they return to the school. The Supreme Dalek team locate the Hand of Omega and take it back to their base where all but one of the slave humans are killed. The Supreme Dalek is revealed to be the little girl who is seen at key points within the episodes.
The Daleks are ordered out to kill the humans but retreat as word of a Emperor Dalek Spacecraft is about to land. The Emperor Daleks leave and go into battle with Supreme Dalek Daleks. When the Supreme Daleks win the battle, the Emperor's call out their secret weapon which blasts through their wall of protection. The Doctor death slides onto the Emperors space craft followed by the rest of the team to disable the ship. Once the Emperors have gained control of the Hand of Omega, they return to the ship orbiting the Earth. The Doctor opens a communication link to the Emperor who reveals himself to be Davros. Ignoring the Doctors pleas, Davros initiates the Hand which leaves the space ship and heads off to the star that Skaros orbits. The planet is destroyed then the hand returns prompting Davros to escape. The Doctor hunts down the Supreme Dalek which self destructs as the little girl faces off against Ace.