The War was fought within the Medusa Cascade and was fought between Humans and Davros's New Dalek Empire. UNIT, Sarah Jane Smith (via Mr Smith) and Torchwood 3 detected 3000 ships entering the Earth's orbit after it's transportation to the Medusa Cascade. These ships were revealed to be Dalek Saucers when they sent a message that comprised of one word, "Exterminate". The Dalek fleet then descended to Earth and caused destruction on a global scale. Daleks were sent to attack all military installations, such as a Unified Intelligence Taskforce base in New York where Project Indigo was researched and developed. The Daleks were able to quickly overwhelm the combined Human forces.
The Unified Intelligence Taskforce was heavily involved in resisting the Dalek invasion fleet, even sending the Valiant to take on the Daleks although it was later destroyed due to the large number of Daleks, with their powerful weapons, that swarmed the vessel.
Martha Jones used Project Indigo to escape from the Daleks in New York City and arrived back in England at her mother's house due to Project Indigo taping into her emotions.
After the loss of the Valiant and numerous other military installations and personnel, the Humans broadcasted their surrender to the New Dalek Empire. Humans were then rounded up by the Daleks, with those who resisted being exterminated, and taken away to the Crucible for an unknown variety of tests and experimentation.
Although the Earth lay in defeat and ruin, Harriet Jones was able to use a undetectable Sub-wave communications network to find and communicate with Torchwood 3, Sarah Jane Smith (again via Mr Smith) and Martha Jones, calling the three different sets of people the "Doctor's Secret Army". After being able to boost the power to contract the Doctor, by using the power of the Cardiff rift and Mr Smith, which in turn caused the Sub-wave network to become detectable. The Daleks were able to locate and apparently exterminate Harriet Jones as she had made it so that the Sub-wave network would only be traced back to herself.
Before her death, Harriet Jones had transferred control of the now-detectable Sub-wave network to Torchwood 3, meaning that the Daleks were now able to locate Torchwood due to the network. The Supreme Dalek then ordered a Dalek Saucer move to attack and destroy Torchwood 3. Gwen Cooper and Ianto Jones, using machine guns, were left to defend Torchwood as Captain Jack Harkness had left to find the Doctor.
Sarah Jane Smith also encountered Daleks when she left her home to find the Doctor. Although she tried to apologize to the Daleks, both of the Daleks replied that the Daleks rejected the concept of apologies or surrender and prepared to exterminate her.
