The Doctor's TARDIS arrived on Mustafar. He made sure the time was right. He should appear before the trial began. He got out and saw speakers on every inhabited corner of the safe rock.
"Doctor" The Master announced, "I have been here for years. In that time I have made a solution to the problem of a simple question, how can I defend my home from people like you? Well I have made the perfect defense system, I have created nanobots that control the magma beneath us"
There was a high eruption of lava. The Doctor simply backed into the TARDIS and let the lava fall on him.

Inside The Doctor frantically worked on keeping the Shields up. So many buttons to press. Even for his Gallifreyan body he felt himself sweat and frantically stress like a human. The TARDIS was never designed for short-range travel by his people, He couldn't use the TARDIS to move closer to The Master, he could miss by a few million miles or even worse, years. He pulled a lever to temporarily de-materialize.
He had to think!

The Master laughing at his victory was inevitably short-lived as The Doctor's TARDIS materialized in the room within arm's range, Opening the door he held his lightsaber out and activated it.
"I know you have a tendency for tricks. Please, come along into my TARDIS."
"How did you-?"
"Took me a few tries but eventually I got it." The Doctor replied
"I could have had a galaxy under my thumb."
"Listen to me, I'm not an expert in using one of these but I have used plenty of bladed weapons before." The Doctor sighed.
The Master started laughing.
"And you thought that in all my time spent on here that I would not have a plan for something like this?"
He moved almost as fast as The Doctor could see and his reflexes were amplified compared to that of a human. The Master's own lightsaber was out and they were both trying to push the other away.
The Doctor tried going for his legs but he jumped. tried going for The Doctor's head. Blocked The Doctor hit him to disorient him. As he was stumbling back he saw a platform directly out the window. He jumped through it. The Doctor after him

The Master pulled out a small circuit.
"Stole it from you I believe... After your final mission for the Time Lords with your second face."
He whistled a TARDIS yet unknown to The Doctor did appear.
"Even if you run" The Doctor said "There's nowhere to go to. You've already lost."
"There is more than one time this entire galaxy will be in political dismay, Doctor. I intend to jump to around about 60 years in the future where all the authorities that wanted me and conspired with me will be dead."
While all of this was happening The Doctor used his sonic screwdriver to tune the TARDIS recall to his pwn. He then whistled.
The Master finally aware of what's happening struggled as the TARDIS formed around him.

Inside The Master was there with The Doctor and the co-ordinates were set for Coruscant.
The Master started laughing.
"What is it?"
"You go through all this trouble to catch me and yet what I was going to do is a fixed point in time."
"But not for today and not for another 15 years!" The Doctor snapped
"Even still how would they feel if they knew you could have saved them, but didn't."
"I couldn't have, it would create a parallel universe."
"Keep telling yourself that." The Master replied. "I once tried that but you stopped me."

On Coruscant The Doctor was immediately greeted by Senator Palpatine.
"This must be The Doctor." He said "And you."
"What's going on?" The Doctor said
"Well he did influence people to start a galactic wide war and conspired with people who are now being dealt with."
There was a split second, making eye contact with one another that The Doctor gave away that he knew Palpatine was lying, then realized he couldn't do anything about it.
"This seems to be a matter for the Galactic Senate, not the Jedi Council."
"But he is a citizen of Gallifrey, Gallifreyan citizens should be judged to Gallifreyan law." Berousa said
"It seems that everyone wants to punish him." Palpatine said "Go ahead, but I want him judged by Galactic rule."
"Yes." Berousa said "From now the incarnation you have will be your last incarnation. You will never again regenerate, but decay and then die."
"No!" The Master said, soon everyone could see an energy, colourless but undoubtedly there flying out of him. Afterwards he still looked the same, if a little bit greyer.
"Accept those terms we do" Yoda said
"I shall judge him accordingly." Palpatine replied. "The sentence for you is death. Thank you for making this sentence a lit easier"
And so The Master was dragged away to meet his fate. With Palpatine walking behind him.

At the Jedi Council building The Doctor walked in but was stopped in one of the hallways.
"Wait Doctor" Yoda said "Met you, I think I did. Earlier in my life, it was. Same face, it was not. Explain, I would like you to."
The Doctor and Yoda continued moving towards the Council chambers.
"I'm a time traveller." The Doctor replied "My life doesn't exactly happen in the order you would expect."
"Have different face, why did you?"
"That's what happens to us every time we're close to death." The Doctor explained
"hmm, interesting, your people are." Yoda said
"Well, one day I shall come back." The Doctor said as they got into the Council room.

As The Doctor and Sarah waved their goodbyes to the Jedi, meanwhile Palpatine was alone with The Master. The doors locked and soundproofed.
"You promised me to rule over the galaxy" Palpatine said "What do I get instead? More ways I have to clear my name."
"I've managed to rule before. I-"
Palpatine threw his Force Lightning at The Master. He was thrown back by the force of it all.
"Do you THINK I would accept your help again?" Palpatine said "Thankfully I know you're on your last incarnation."
The lightning stopped as The Master stopped breathing. He coughed then got up, burned to a crisp. He pulled out the still working TARDIS recall device. As Palpatine shocked him again The Master's TARDIS materialized around him.

The Doctor and Sarah Jane were saying goodbye to that Galaxy.
"Doctor, what happens next?"
"Did you notice that The Jedi Council are their own authority without any oversight and a personal army?"
"N-No."
"Well what happens is a Senator named Palpatine eventually becomes Chancellor and then he orders a clone army and eventually double-crosses The Jedi, killing a lot of them and then a fascist Empire rises and after that is destroyed... It's all a messy business and quite a lot of it is fixed I'm afraid."
"So all we did, was for nothing?"
"I wouldn't say that." The Doctor replied, "I set a lot of things in motion today and some of them lead to more Jedi being on their guard for when something like this happens, because of that threat, more survive Order 66."
"So you changed history?"
"My dear girl, I've been changing history since the beginning." The Doctor replied.