The battle of the machine brain was a Dalek effort, with the aid of the First Doctor, to stop the machine brain from producing enough Neutronium to destroy Skaro, and unleashing enough radioactive dust to reach Earth.
In the deserts of Skaro, the Dalek scientists ordered the machine brain to produce vast quantities of Neutronium, the most dangerous nuclear substance. This was their last order, as the machine destroyed the scientists and the death rays protected the machine from being tampered with, leaving the Daleks without any way of stopping it. If it kept producing Neutronium, it would reach a critical point and explode, taking Skaro with it.
A Dalek deliberately allowed an Earth-bound spaceship to capture him so he could contact the First Doctor to help Skaro. Realising the urgency, the Doctor smuggled the Dalek aboard a spacefighter and rushed to Skaro. A Dalek squadron, unaware of the impending catastrophe, shot down the Doctor's ship. After crash-landing in an area inhabited by two-headed monsters, the Doctor was brought to the Dalek capital and briefed on the conflict.
The Doctor ordered a suicide squadron of Daleks to attack the machine brain with explosives that would not set off the machine's Neutronium. The attack had no effect. The Doctor approached the machine brain on his own, and was unaffected by the death rays, as it was only harmful to Daleks; the Doctor was unaffected "apart from being hot". He switched off the power, leaving the machine silent. (PROSE: Doctor Who and the Daleks)