"I didn't see him until well after the war ended. At the end of the universe." The Doctor shrugged, trying to wrap his mind around the concept of the Master being sane. And devoted to anything other than universal domination and/or destruction. He really hadn't figured out which the Master wanted more.
"He stole my TARDIS, I chased after him with Jack's Vortex Manipulator, and Jack and Martha. Spent a year of hell working on a plan to stop him, stopped him, held him as he died, instead of regenerating. Burned his body, mourned, went on best I could. Picked up new companions, regenerated. Haven't looked for him since. Not yet, anyway."