Board Thread:The Reference Desk/@comment-67.159.143.245-20150525014248/@comment-188432-20150603173813

Well, your question is massively broad, as the defining characteristic of the Doctor's TARDIS is that it does malfunction with great regularity. When we're first introduced to it in An Unearthly Child, it's on the fritz, and the Doctor has returned with what he thinks is a suitable replacement part.

And it's been on the blink ever since. A lot of the time we don't know why it's malfunctioned — just that it has. But it's been variously out of mercury, out of Zeiton-7, throwing fault indicator lights, piloted by an incompetent Doctor, or simply grumpy. To make things more complicated, The Doctor's Wife suggests that the TARDIS, a living being, has pretended to be faulty when she was really deliberately guiding the Doctor to a particular spot for reasons of her own.

But if you're asking specifically about Rise of the Cybermen, the reason for fault there is pretty straightforward. The TARDIS has found itself in an alternate reality that's simply incompatible with her. She essentially "shorts out", until the Doctor can share some of his regenerative energy with her and jump start her.