Ousted from his own TARDIS! It stung badly enough when the Master stole her, leaving him stranded with Jack and Martha at the end of time, reliant on Jack’s vortex manipulator to transport them back to the past.
That was nothing to how he feels now, wizened and shrunken, locked in a cage. The TARDIS is his and he is hers, but the Master has corrupted her into something unthinkable, evil and perverted: a paradox machine.
It’s so wrong; he longs to go to her, comfort her, restore her to her former glory, but all he can do is wait.