The Doctor was pretty sure that this conversation would be going entirely differently had he been speaking with the Master instead of Missy. Instead of angry and defensive, Missy was gentler and sympathetic, which was what the Doctor sorely needed now.
He was quiet while listening to what Missy said, not arguing, not agreeing, (even though he did agree with her). Instead, he was much more fascinated by the tenderness she expressed. Smitten. When she finished speaking, instead of addressing her points, he began telling her something entirely different.
"You'd been arrested and sentenced to death. The [people who were in charge of her execution, I couldn't find the names of them online anywhere] had called me to do the deed, since it's custom to have a member of the condemned’s species perform the execution. I was the only other Time Lord left, there was nobody else to do it. But moments before it was scheduled to happen, I was interrupted by a message from River Song, which inspired me to go through with doing what I had planned on, anyway. Which was to change the settings of the machine so that instead of killing you, it only weakened you. I'd promised them that I'd watch over your body for 1,000 years, but I didn't specify whether your body would be dead or alive. The vault that was meant to keep your corpse, became.... well... your cell." He knew that wouldn't go over well. "But I tried to make it as comfortable for you as possible. I'd hoped that I could... help you understand, to change you for the better. There were times when I thought I succeeded. There were glimmers of empathy and kindness." He fell silent. "But in the end, when I begged you to stay and help fight the cybermen to save innocent lives, you left me to escape with your previous regeneration, the Master."
A pause. "I don't know why I'm telling you this, except... I think it was important for you to know. You were probably wondering, anyway."