The Doctor never fought in the Time War but the Master did. I'm not sure all the exact details yet, but it'll probably use character seen in New Who (namely John Simm's Master and Chris Eccleston/David Tennant's Doctor and probably Rose) while ignoring most that happened in series 1-4 because it's AU.

Vengeance
Chapter One

The War was over and yet it wasn't, part of the Master knew that it would never really be over. His mind was still fresh full of images of the torture, the screaming, the burning, the death and destruction. He could do nothing to stop the images, bright orange flames still seemed to flicker in front of his eyes, attempting to burn his already dying body, succeeding in clouding his vision to what was really in front of him. He could still smell the horrific stench of burning flesh, could still feel the dead weight of the people he'd tried to pull to safety. But it was over. It was done. He had ended it. The planets wide destruction was over, Gallifrey had been destroyed. By him.

He stepped into his TARDIS, though fell may be a more fitting word, but the familiar sight was of no comfort to him. He closed his eyes in a feeble attempt to block out the images, but they just continued to play on the inside of his eyelids. He wished he could turn off his senses; stop hearing; stop smelling; stop seeing; stop feeling. He quickly became aware of the pain, the unbearable pain, the unstopping pain that covered every millimetre of his body and wouldn't let up even slightly. The pain that he didn't want to let up, the pain was all that was left of Gallifrey; it was all that was left of the destruction. It was all he had left, he hoped it would never end, it was all he knew. Everything he remembered was; pain; hurt; aching; death.

He couldn't stop the regeneration, his body forced the change upon him without his control. He screamed, the sound expressed all the emptiness and shock and pain that he was feeling, the sound perfectly mimicked the screams of those tortured and killed in the Time War. He remembered all his previous regenerations, all the times he had taken someone's body in a desperate attempt to stay alive. He had always wanting to keep on living. He could feel everything changing, his hair shortened and became a lighter colour, his whole body morphed into another he became physically younger and smaller. Everything about the way he looked changed while everything underneath remained the same.

He let out a quieter more desperate scream as the regeneration ended, once again it had not been in his control, it had just happened. He reached for the control panel to try and steady himself but he missed and fell to the floor. He was barely conscious and had no energy whatsoever. Tears pricked at his eyes as he lay there overwhelmed by everything, but he forced himself to ignore them and focus on the pain. He forced himself to focus on the way all of this made him feel; the terror; the desperation; the pain; the anger. The anger consumed him, he wanted someone to understand, he wanted someone to feel his pain. Why should he be the only one to feel like this?

He lost his battle with consciousness, pure exhaustion due to a timeless time spent fighting caused him to fall into a soft sleep despite all the horror and pain circling his mind. Time had no meaning in the TARDIS but he slept was a necessary amount of time. It was when he woke that he heard it first. The drumbeat. The four taps repeating over and over in his head. Taptaptaptap, taptaptaptap, taptaptaptap. Continuously in his head, never pausing, never stopping, just drumming. He put his hands in his ears to block it out, but it didn't stop, it was inside his head, he couldn't stop it.

He felt a hatred build up in him and he made no attempt to stop it. He hated the Daleks for causing the Time War. He hated himself for surviving it. He hated the Time Lords for not being able to stop it. He hated the other planets that got involved for their helplessness. He hated all the planets that didn't get involved for not helping. He hated everything and everyone. He wanted to hurt something, anything, everything. He jumped up, ignoring the light-headedness he was still feeling, and thumped the console in sheer frustration. The TARDIS gave out a little groan and the Master laughed at it. It wasn't enough, it didn't even begin to scratch the surface of what he wanted to do. He needed something bigger, something more.

To begin with he needed a whole new identity. He needed to be himself, but not. He needed to be able to act naturally, to ignore the drumming, to ignore the memories of the War. He needed to become the Master once again. He headed straight for the wardrobe and picking an outfit proved to be difficult. He wanted to look authoritative but not completely unapproachable, powerful but not too upper class. In the end he settled for a simple black suit with no tie. Looking in the mirror he realised he was younger than he had ever regenerated before, and he looked scared. Time was the one thing he had, a never ending stream of time, but it wouldn't be enough to leave it behind. The Time War would always be there, fresh in his mind. He ran his hands over his face, changing his expression by the time he moved them. He could be powerful again, he could be Master. He would be Master. The young innocent look about him would just help him along the way. The suit, thankfully, worked exactly how he wished it to. He was going to fit in perfectly on Earth, which was his next stop.

The Doctor always loved Earth in a way the Master couldn't understand. It was just a water covered tiny little planet full of stupid, closed-minded cowards. He paused at that thought, laughing almost manically to himself, of course! The Doctor loved the planet so much because he fitted in there so perfectly. A coward like them. The one who ran away, the one who always ran away right from when they were children. He remembered them both being taken to the Untempered Schism, the Master had stayed and watched, amazed and hypnotised by the insane power of it while the Doctor had looked only for a moment before running away traumatised. The Doctor; a healer; the one who made things better, they had been enemies since they left Gallifrey for opposite reasons but the Master had never hated him. Now he did, when the Doctor chose to let fear overtake him and run away when his planet; his people most needed help that's when the Master began to hate him. He was a coward but worse than that he was a traitor. Doctor? That was a joke, he hadn't helped Gallifrey, he hadn't even tried. The Master made a promise to himself there and then that if he came across the Doctor, he would teach the coward a lesson he would never forget.

For now, though, he had more important things to do. He set the TARDIS coordinates for early 21st century Earth and sat down, waiting for arrival.