They survive against all odds. Always. It doesn't matter what they face or what their circumstances might be. It doesn't matter whom they fight; they survive. They survived when their body was a walking corpse -stealing another's body. Nyssa's father's body.
They survived the fire. The Doctor had condemned them; let them to die in the flames. But they had showed again, much to the Doctor's relief. He had hopped against hope for the Master's return even when it seemed impossible.
They survived the Daleks. They came back from the Eye of Harmony. They came back, always came back from impeding dead. They were a constant, his constant.
The Doctor had come to not only accept this truth, but to relish and hope for their return. The Master had come back from the dead as if it was nothing, or their gig - the Doctor had cried for them, had begged them to regenerate to no avail.
The Master refused as they always did. The Master would only behave according to their terms, not to the Doctor's whims.
They had come back and in the blink of an eye they were gone again.
The Doctor feared their death no more.
The Master would come back as they always did. The Master were wearing another face - the Mistress or Missy as they call themselves now - but they were the same old friend.
"Run, I said!" the Doctor repeats himself without looking at the Mistress. Clara is his only concern. Clara' safety is his priority, because his companion's well-being is always first - except when it's not.
But even then, he worries.
"That wasn't me. That was always you, Doctor," the Mistress says, but them turn and walk away from the Doctor.
The dignity of their walking away doesn't fool him, but he has other things to worry about. He always has.
As the Doctor takes Clara to the TARDIS and the doors seals shut behind them, he hits the dematerialisation button and forces himself not to think of the Mistress.
He goes back and helps them the only way he can - his way is mercy and forgiveness. The Mistress' way is a killing spree that will get what they need.
Clara doesn't look at him - she knows better now, after all the evidence that points what exactly is the Doctor's opinion of the Mistress. He can says he doesn't want the Mistress to live, but he turns a blind eye to whatever the Mistress does to survive.
The Doctor counts on the Mistress to save themselves. He counts on the Mistress' intelligence and self-preservation to keep them alive.
The Mistress is not without means to save themselves. The Doctor knows they'll see each other again. They'll fight across the stars and constellations, across time and space like they had always done and will always do. Mistress and Doctor, Doctor and Mistress.
Whatever their face, they will always be the Doctor's dearest friend and best enemy.