The pipe had started off as an affectation. He was an old man in appearance and by human standards, so he was expected to smoke a pipe. On Gallifrey, his smoking would've been yet another sign of youthful rebellion which would've warranted comments that were the Gallifreyan equivalent of an exasperated exclamation of "Teenagers!".

Most people, upon learning that he'd smoked and that he'd quit, would've expected the reason that he'd stopped smoking had had something to do with the misadventure that his attempts at lighting his pipe back when he'd turned up in the stone age had led to, seeing as it had gotten him kidnapped and nearly gotten him and his companions at the time killed. The truth was that he'd actually quit smoking shortly after his first meeting with the Daleks, and it had been because his smoking had nearly gotten him killed another way.

What had happened was that Ian had watched him struggle to light his pipe with an uncooperative lighter and decided to be nice.

"You might find these a little easier to light," Ian had said as he pulled a slightly rumpled pack that was three quarters of the way full of cigarettes out of his pocket. "I confiscated them from Jimmy the day we left, and I don't have a use for them."

Since he didn't have to tip the lighter sideways like he would've with the pipe which really should've been lit with matches, the cigarettes proved to be marginally easier to light. They also proved rather easy to forget about as well, and since the burning tobacco wasn't mostly safely contained in the bowl of a pipe...

Let's just say that the statistics regarding the number of people who dozed off while smoking and accidentially set themselves on fire went up by one careless individual who woke up to Barbara and Ian frantically attempting to smother the flames with a blanket.