During a conversation with Rusty the Dalek in ‘Into the Dalek’ the Doctor reveals something of his past. Until he travelled to Skaro he was just calling himself the Doctor. Afterwards he realised that the Doctor must not be the Daleks.
It has been observed before that the Doctor we meet in ‘An Unearthly Child’ and his first adventure with the Tribe of Gum is not the man he would later be. It is interesting that his encounter with the Daleks would be so pivotal to defining who he would be.
In ‘The Daleks’ the titular race were scientists, not above manipulating others. These are traits that the Doctor shared, tricking Ian, Barbara and even his own granddaughter into exploring the Kaled city.
This seems to have taught him a valuable lesson and made him vow to never use others in such a fashion. To never let his quest for knowledge overcome his humanity. There isn’t a radical transformation, so at that point it was probably just something to muse upon but it planted the seed.
‘The Daleks’ almost didn’t make it to the screen, as ‘The Masters of Luxor’ was due to be the second story. Give the significance of the encounter of Skaro this could be seen as a manipulation of the Doctor’s past in order to turn him into the hero the universe needed. The TARDIS or Clara might have arranged this prod in the right direction.
Alternatively someone could alter this moment so that ‘The Masters of Luxor’ occurs instead. PCs might encounter a very different Doctor and need to find the point of divergence to put him back on track.
It might be that the Doctor deliberately sought out the Daleks. Initially he gave the impression that they were unknown to him but later evidence would suggest that both he and the Time Lords were aware of them for quite some time.
The Doctor might have wanted to meet them to compare himself to them. He might have seen something of his own people in them, hiding themselves away and afraid to leave the safety of their city.
‘The Dalek Invasion of Earth’ could have illustrated to the Doctor that he couldn’t be reactive. Evil would continue to spread through the universe unless it was opposed. This could be key to why he abandoned Susan, realising that he’d have to run towards danger now.
If he was comparing the Daleks to the Time Lords these events and those of ‘The Dalek Masterplan’ could have suggested just how powerful and dangerous the Time Lords would be if they ever decided to leave Gallifrey (as the Time War would later illustrate).
His first adventure as the 2nd Doctor would bring him back into contact with his foes in ‘The Power of The Daleks’. For the first time they posed as willing servants, with the Doctor seeing through their ruse.
How might his own self image have been shaken if the Daleks were capable of change? How would he define himself if a Dalek could be good? His very identity depended on them being evil.
‘The Evil of Daleks’ shows the Doctor introducing a human element. This could be enough attempt to test whether the very nature of the Daleks could be altered. If nothing else it showed that it was possible to divide them.
In ‘The War Games’ the Doctor brings up the Daleks at his trial. He describes them as the worst of the races he has fought, berating the Time Lords for only observing them. The Doctor might have been more convincing than he realised here.
Could this have been what convinced the Time Lords that the Daleks needed to be eradicated. Did this put in motion the events of ‘Genesis of The Daleks’ and eventually the Time War?
Part of the 3rd Doctors memories were wiped. Could this to be cover up the missions that the 2nd Doctor performed for the Time Lords to destroy the Daleks? Like the War Doctor this could be a period of his life he was only too willing to forget.
The 3rd Doctor’s exile could have been to keep him safe from the Daleks, since they were not supposed to be active in the UNIT era. Whenever he did encounter them it was due to time travel.
The importance of the Daleks to the Doctor adds new light to ‘Genesis of the Daleks’. Here he hesitates in changing their timeline, arguing that things could be better because of the Daleks. His hesitation could have been based on the knowledge that his own timeline could be altered.
The introduction of Davros gave the Doctor an individual to compare himself against. So many times he’d mock the Davros for loosing more and more of his identity each time they met. Was this a commentary on how the Doctor was loosing his own identity each regeneration to his quest to be everything the Daleks weren’t?
‘Genesis of the Daleks’, with its fascist imagery, consolidates the Daleks as soldiers rather than scientists. The Doctor would similarly be accused of changing his role, turning his companions into soldiers and changing the very definition of his name to mean warrior.
Indeed the Daleks would bring out the worst in the Doctor. Even the relatively meek 5th Doctor would gun down kaled mutants while the 7th Doctor would destroy Skaro itself to be rid of them (tricking Davros into doing the dirty work for him).
In both ‘Dalek’ and ‘Into the Dalek’ his mortal enemies recognise him as one of their own. ‘Asylum of the Daleks’ revealed that the Daleks view the Doctors hatred for them as beautiful.
Which ultimately reveals that the Doctor couldn’t and can’t live up to his vow while the Daleks exist. As long as they do hate with define them both, eclipsing the beauties of the universe that the Doctor believes are inside him.