The Daleks' Timeline

The answer is simple: time can be re-written. Steven Moffat has shown us the way!

The Doctor has indeed met the Daleks for the first time in the 1963 / 1964 story The Daleks. At that point in time The Daleks were barely survivors of a long war with The Thals. They assumed their planet held the only life in the universe as per their long dead creator Davros. They had developed enough to travel within the confines of their city whilst hoping to eventually leave their casings behind.

Many years later in the Doctor's timeline the Timelords, knowing of the Doctor's meetings with the Daleks and fearing that the Daleks may prove a threat to themselves, send the Doctor back in time to either destroy or alter the Daleks in order to neutralise them (Genesis of the Daleks). It's this very act which causes the Daleks to develop in a different way. Davros learns that aliens do indeed exist, that he himself is not part of the Dalek successes / defeats and sets out to protect himself whilst altering the Daleks in order to better prepare them. It's possible that Davros' early Daleks, albeit able to travel outside the city on ground, ultimately became irradiated when outside and driven mad. In a timeline where the Doctor doesn't visit Skaro at this point, the Daleks rebel, kill Davros and bunker down in the lower depths of the city. They cannot leave the city through fear of madness / death and therefore re-develop their casings to work on static electricity rather than other power-sapping methods. They re-build the city upwards with floors / walls of metal which they believe they cannot leave. Many years later the Doctor, Ian, Barbara and Susan arrive (The Daleks).

With the interference of the Timelords everything changes: they themselves are the cause of the Daleks' universal conquest ambitions and the great Time War begins. Davros, having met the Doctor, quickly upgrades his life support systems in expectation that he may not be around for much longer otherwise. The Daleks are quickly programmed with knowledge of the times they have met the Doctor in spite of any tape recording of those times having been retrieved and destroyed. Once the Doctor has gone from Skaro the Daleks still bunker down, then rebuild the city and stay in it until such time that they can safely leave it. The Doctor, Ian, Barbara and Susan arrive (The Daleks) but the Daleks at this time are still reliant on static electricity. Knowledge of the Doctor's previous visit is barely known if at all to the creatures who exist at this time; Daleks don't live forever and differing generations have existed by this time, yet they know of an attempt to destroy them many years before. At the end of that story their power source is destroyed and our heroes leave. A backup power system has already kicked into operation and the Daleks live. They bide their time and once radiation levels have lowered to safe levels can use casings that can travel on land. The Daleks leave the city and the Thals, who know of space ships from seeing the Tardis, have developed a way of getting off the planet. The Daleks now have Skaro to themselves and their plans for universal conquest are born. They know of the Timelords and of the intent to destroy them many years back and it is the desired destruction of the Timelords which leads the Daleks to conquer / destroy all other species. Davros' body is still in the lower depths of the city but over thousands of years regenerates.

The more the Daleks travel out into space the more they hear of the Doctor, the more times they meet the Doctor they learn he is a Timelord. The know it is this species which tried to destroy them many years before. It is to time travel that the Daleks turn to in order to defeat the Timelords. They become interested in tracking the Doctor down hence The Chase is part of the Time War. However, it is the first Doctor they track through time, he not knowing at that point that a Time War is raging. It is some point after end of that story that Tennant, Smith and John Hurt's Doctor explains to the 1st Doctor what's happening and enlist his help for The Day of the Doctor.

In his second incarnation the Doctor meets the Daleks and on Skaro manages to turn the Daleks against each other (The Evil of the Daleks) and their great city is almost destroyed. The Daleks abandon Skaro at this point. Hundreds of years later the 4th Doctor arrives (Destiny of the Daleks) and at this time in the lower depths of the ruined city Davros revives. The Movellans are a robotic race designed to stall the Daleks' attempts at universal conquest and halt the Time War. Once Davros has escaped from the space ship in Resurrection of the Daleks the Time War enters a new phase with Davros leading the Daleks albeit with factions of Daleks still against him. At one point he has to hide out at Tranquil Repose (Revelation of the Daleks) at a time when the Daleks are losing the Time War. However, Davros leads them to greater strength by returning to Skaro and likely rebuilding an army there. Davros is killed in battle but is saved by Dalek Khan who has managed to break through a fixed point in time.

I'll likely expand on this section to include all Dalek stories once I've finally lost all sense of reality.