Throughout the course of that dark year where The Master ruled the human race with an iron fist, a number of events happened which glided gracefully under the noses of those closest to him. Even Lucy, his obedient trophy wife, was completely ignorant to the abditive occurrences happening outside of her sphere of influence. Of course, if knowledge of these events was somehow leaked to the public down below the overcasting, nefarious shadow of the superior skyship, each plan of either Time Lord would surely be spoiled, those plans being the destruction and the protection of the human race, and though their separation is retained, the line which differs the two could be blurred through the eye of the history which either had trailing in their wake.
It is true that The Doctor spent the good part of those 365 long, painful days in the constricting confines of a standard wheelchair. He could only cover short distances on his feet, so escape was surely out of the question. Even so, the drop was far, his TARDIS was unattainable and Jack's vortex manipulator was in Martha's hands and completely out of reach, not that he'd be caught dead using such primitive travel willy-nilly. Nevertheless, with a plan in action, he had no choice but to wait those days out, hour by hour, and though the curse of age plagued his face, beneath the surface of sorrow and impatience, his brown eyes recalled the youthful and adventurous glimmer in which he thrived upon.
Time seemed slower than ever, though The Doctor had not quite experienced such a tethering since the Time Lords bound him to the earth's surface so very long ago. It felt unnatural to him, allowing each second to tick in such a linear fashion. His species found sport in manipulating the time vortex, and without that luxury at the tip of his screwdriver, The Doctor was no less forced to sit through each grueling minute. He spent most of his time peering through his favored small window, unwilling to stress his creaky, withered bones. He had made the conclusion that his old friend found sadistic pleasure in witnessing him suffer through the days, that being the only probable assumption for how The Master could stand such slow-passing time. Although this theory disqualifies the fact that he had spent time similarly for countless years while bound to the same body and the ignorance to his true existence, though the thought of it was absolutely outlandish to The Doctor.
The Doctor, of course, blamed himself for these events. It was he who took Martha, his companion, in. And it was he who taught her the way a Time Lord could confine his true essence to a special sort of pocket watch. If he had never offered her a lift she never would have come to the point where she had second guessed that mysterious silver watch with those peculiar alienish circles scrawled in to the metal. In fact, she never would have been on the ship to Utopia in the first place, rather safe at home with her family where she belonged, pursuing the career of a doctor. A real, proper doctor. Therefore, in a roundabout way, he had brought this all upon himself. Of course, he had always brought these things upon himself. Running could only take him so far. His past was bound to return and, regrettably, backfire as it always had. He felt pity for his old friend, who could have died happy, with a successful human life behind him. The Master could have perished in ignorance, free from the curse of the Time Lords. Free from the crushing weight of being the last of two left of his own species. But alas, things were never quite that easy for The Doctor, he supposed. Though he had spent the better part of his adult life avoiding the childhood friend of his, or cleaning up his messes, The Doctor nevertheless had always wished for a better fate of his friend. A moment of relaxation, perhaps, free from the endless drumming. If not himself, why not a person in which he cared deeply for? He had accepted long ago that he could never quite end his reign or perilous running, but he could end it for others.
The truth was that he cared deeply for his fellow Time Lord, and he had a hunch that The Master felt similarly. As childhood friends, regardless of their inability to see eye-to-eye in most situations, they clicked wonderfully in every other way. The last of their kind, brilliant, and entirely mad. Where they were different in one way, they were the same in a thousand others.
That, above all, is the reason The Doctor, though standing his ground confidently in that year, had also learned to forgive his foe and friend.
Not because he was kind, though he was in every way imaginable.
Not because of loneliness, though loneliness was the only constant in his life which he could rely on.
Because if he couldn't forgive himself, he had to learn to forgive his equal.