The TARDIS is a mere shell of her former self, wiring torn out, spliced, reconnected in unnatural ways. She’s been twisted and warped into an abomination, and she claws at the Doctor’s mind with her freakishness worse than Jack ever did.
But it’s not her fault, it’s the Master’s; he’s the one who did this to her, and the Doctor can feel her suffering. She hates what she is, what she’s been forced to do, maintaining a paradox. She’s crying out to him for help.
It’s not in vain.
Restoring her will take time, but he’ll do whatever it takes.