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Of course they were not made for each other. He was intended to serve his planet and his people without diversion or question. She was meant merely for a tool, a means to get from one locus of activity to another with the minimum of fuss.
A generation of Timelords used her so, never looking to the side, to see the universe that she could have shown them.
She didn't care about them. She laid the Time Vortex out like a path before him, persuaded him so skilfully that for a thousand years he thought leaving was his own idea.