The Doctor and his travelling companion, retired army officer Alistair Lethbridge-Stewart, take a random trip in the TARDIS - and land on the planet Skaro. The Doctor helped the Thals to defeat the Daleks years ago, so he is surprised to find the Thal city under Dalek occupation. He determines to help them again, but what is the Daleks' purpose in keeping the Thals alive? Does it have anything to do with the Daleks' mythical creator, named in their teachings as Davros?
The Dalek/Thal war being caused by a third alien race, and Daleks being capable of coexisting with the Thals, were elements dropped from Terry Nation's original proposal for TV: The Daleks. 
The Thousand Year War and Davros' history are different (to the proper timeline), most notably that the war was considerably shorter than a thousand years and started closer to the end. The Quatch's involvement - and the Quatch themselves - do not seem to be caused by any difference in the Doctor's timeline.
The Daleks seen in the story were created by Davros to have a degree of compassion so they would not turn on him. This led to them developing the idea that because Daleks were superior to all other life, they had a duty to protect that life. When Davros left Skaro, most of this second batch went on a quest to find him; they returned after the events of TV: The Daleks and enslaved the unprepared Thals, in order to protect them from the Quatch. They make them work to strengthen them (via a process of social darwinism) and to strengthen the Daleks, thus protecting the Thals by making the Daleks stronger.