This is how I imagine the Doctor's death. See, I can't imagine him dying n some grand way where the whole universe stops to take notice and mourn. That simply doesn't seem the Doctor's way. WARNING: THIS IS VERY SAD! It is his death scene, so, DUH. If you can't handle sad, walk away. Then again, if you can't handle sad, I don't think you should be in this fandom at all. Oh well, here goes.
There has just been a battle, the biggest battle in the Doctor's history, a battle for Earth between the Doctor and all his enemies; from Daleks to Cybermen and all the lesser enemies between. The battle is over now and the dust is settling. The lesser enemies along with some of the Doctor's friends and many humans who had joined the fight, were all standing in a large ring where the Doctor was just fighting. All is still and quiet as everyone takes in the scene before them. Daleks and Cybermen are everywhere, scores of scattered around inside the ring. And in the center of it all, is the Doctor, standing triumphant over the lifeless husks that is all that remains of both races. After so long, the Doctor has finally defeated his two greatest enemies. Daleks and Cybermen are now extinct. He looks at the others, all his enemies, frozen in place, too afraid to move, for they have just witnessed him annihilate his two strongest foes. He speaks.
"This planet and these people, are precious to me. No one should ever expect to come here and harm them, without expecting to face me first. Now is your chance, all of you, leave this planet now, do not intervene with humans ever again, and you can live. That, or continue fighting, and one by one, you will all die." And his enemies turned tail and ran, finally admitting that they could not defeat the Doctor, and reserved to never trying again. As the last enemy left, the humans cheered. All who had gathered and fought cheered for the Doctor, their savior. And he walks away, going back to his Tardis as his friends follow.
(Insert companion's name here) is exited and absolutely full of energy. "You did it! You really did it Doctor! You are amazing! But, what now?" He doesn't answer. He just walks up to the console and flies the Tardis. One by one, he takes all the friends he had gathered home, (Insert companion's name here) last, until the only ones left on the Tardis and River. (Don't ask how she's there, I just imagine she is somehow.) He flies the Tardis once more and when she lands, he stands there, leaning on the console. He takes the sonic screwdriver and the Tardis key out of his pocket and sets them there. River walks up and gently touches his hand, tugging it off and away from the controls. He smiles faintly at her, sadly, and hugs her as she hugs back. They stand like that for a few moments before he falls into her, unable to hold himself up anymore. She sits on the floor, holding him, crying silent tears with him. She doesn't ask what's wrong or how can she help, because she knows.
She's his wife, she's River Song, and she knows, just as he does, what is wrong and that she cannot help this time. Because the Doctor is old. He is old and he has lived a long life, a good long life. And in that life, he has had many brushes with death though which he lived, but not this time. The body of the weary old Timelord had finally hit its limits. It simply could not carry on any more. The Doctor was dying and this is where on the Fields of Trenzalore. After (x) years the Doctor passed, not with a yell or a flash of light, but quietly, with a breath no one else in the whole universe would hear, in the arms of his dead wife as witness, in the Console Room of the Tardis no one else could enter, the Doctor died quietly and no one ever knew.
And yet, as it turns out, this was the last, and perhaps the greatest, gift the Doctor could give the world. Not his life, lost in battle, but his memory. For those enemies would go forth from that battle and they would spread the word of The Human's Great Defender and with everyone believing he was still alive and fighting, no one would ever dare intervene in human history again.