The Doctor continued running and found the two Jedi in an alleyway. looking confused.
"What is it?!" The Doctor asked
"We couldn't see him clearly but he ran into a dumpster and vanished."

Immediately he looked up and saw The Master on the roof.
"Well well, Doctor. You have meddled in my affairs for the last time."
He aimed a pistol at him and fired. The Doctor leaped out of the way and started climbing the ladder where he was running away from. The Jedi were able to leap that high and was already after him. He was heading towards the shipyard where the first body was. The Master was able to get into a one-man ship and start flying. The Doctor got into another one-man ship while The Jedi got into a much larger ship.
"Doctor come with us!" Obi-Wan said
"He'll use any advantage." The Doctor said "That includes the size of his ship!"

The Master was flying at top speed. swerving through traffic both vertically and horizontally. He eventually pulled up leaving the planet itself. The Doctor followed.
"Space Settings: On" The ship's computer said. He saw he was running out of fuel. He saw The Master escape by joining a much larger ship.

At The Jedi Council The Doctor walked in.
"He has help." The Doctor said "Can you give me the names of every group that would aid him in his egomania?"
"Blind, we may be." Yoda said "Came to our mind, nothing did."
"What if I told you there maybe someone plotting in the shadows to aid him. Someone that could know about his escapades and has the wealth to buy a ship large enough to contain this entire building."
He looked around.
"Where's the old man?"
"Dooku is gone" Mace Windu said "He said he was to help his apprentice in capturing your fugitive."
"Dooku?" The Doctor said "I never saw him."
"And neither did I." Qui-Gon said "I did sense a Dark Side aura from him."
"Could he have done something like that?" The Doctor said
"Yes." Qui-Gon said
"I believe in innocence until proven guilty." The Doctor said "However, I would like to lend a ship of yours after investigating a way to follow the ship's trail, I also suspect if he's responsible for that then he may also be the reason for my missing companion."

He was able to comandeer a ship from The Jedi. This one was much larger. The Doctor let the Jedi fly it. They tracked the person who owns the larger ship The Master got into. It was The Trade Federation. The Doctor felt that he may have come here too late considering his resources. He walked to Obi-Wan Kenobi.
"I'm sorry but if Dooku has betrayed you-"
"We'll get him." Qui-Gon said "He maybe my old master but we have to. It's our way."
"I understand" The Doctor said "This Trade Federation, does Dooku work with them at all?"
"Yes." Kenobi said "In fact, it's him that we appointed to see if there's any corruption inside the institution."
"Then I may fear the worst." The Doctor said "Is there a spare lightsaber on board?"
"Yes." Qui-Gon said, he walked away and brought one back.
"We may not want to start a confrontation Doctor." Qui-Gon said
"I would like to be prepared." The Doctor replied
"It is not in our way to kill without cause. We are keepers of the peace."
"My race are time travellers, it is in our way to not interfere with history." The Doctor replied "The one I'm chasing is interfering, the result may cause ripples throughout this galaxy and maybe even bigger."
"Isn't what you're doing interfering as well?" Obi-Wan asked
"No, I'm setting things right." The Doctor said.

The Master and Count Dooku were on the ship of The Trade Federation.
"Gunray." The Master said "If your boss didn't say anything then I am his second-in command."
"I have heard about you." he said "What did you want from us?"
"Safe passage to Yavin 4 only. I left something behind on my last travels."
"That interrupts our-"
The Master started using hypnosis "Now, you will obey me. Correct?"
"Correct."
"We will go to Yavin 4. I need to pick up something from there and drop some human cargo off."
"Human cargo? The place is nothing but jungle and swamp."
"Count Dooku will verify what I have to say."
"I don't know what he has to pick up from Yavin 4, but to me a good place to hide would be Genosis."
"I'm not hiding." The Master replied "You can lay low there, I would have further need of you later."
"Is what you're picking up from there a weapon of some sort?" Dooku asked
"No. I'm still aiming for subtlety, a weapon that wipes out planets is crude."
"Well, what are you going to do then?"
"Dooku, because this ship moves slower then something The Doctor and the Jedi would be using my idea would be to call off the attacks and make up a lie about his companion."
"They won't believe me." Dooku replied "I know what to do otherwise."
"How about you instead tell them you were captured by me." The Master said
"They wouldn't believe it."
"I have my ways. The Doctor might believe you." The Master said
"And if he doesn't?"
"Well, we have defenses here not even The Doctor could survive if they're attacked."

Count Dooku walked to Sarah Jane Smith, guarded by battle droids and Droideka's.
"How could you betray them for him?" Sarah asked
"I haven't. I have grown weary of trying to keep the peace." Dooku said "I am thinking of other methods to use so everybody remains in line."
Dooku then outstretched his hand. Sarah Jane could feel something inside her mind, as if he can control it.
"Who is The Doctor?" Dooku asked
"He's a time traveller." Sarah Jane replied, shocked that she has no power to stop herself from telling the truth.
"And The Master, he's a time traveller too?"
"Yes." Sarah Jane replied
"Why is The Doctor here?" Dooku asked
"To stop The Master." Sarah Jane said "His species is trying to stop him from making an event in history happen early."
"So to you, this is ancient history?"
"No. I'm from another planet."
"The same place The Doctor comes from?"
"No. I don't know where The Doctor's planet is."
Sarah was trying to stop herself but she couldn't.
"This event The Master is trying to make happen early" Dooku said "What is it?"
"I don't know." she said, exhausted
"That's all." he said before turning around and leaving.

"I know what you're doing." Dooku said
"Do you now?" The Master replied
"I also know of The Doctor." Dooku said "If he's like you then that shouldn't be a problem."
"Then you know what I'm recovering from Yavin." The Master said
"Your time machine?"
"TARDIS Time and Relative Dimensions In Space."
"To you, this is all ancient history?"
"No. Time seems to work differently from a non-linear perspective."

The Doctor could see The Federation ship. It was going to Yavin 4 according to the map.
"We aren't looking to start a fight here Doctor." Qui-Gon assured
"This is The Doctor." The Doctor said on the communication channels "I am here with 2 Jedi, I am here on a diplomatic mission from across galaxies to retrieve a fugitive that maybe hiding in your midst."
"Doctor." Count Dooku said "The Master seems to have taken over this ship. I have your companion, she is safe with me."
"Master." Qui-Gon said "I knew there was an explanation."
"The Master is leaving with another ship, he is going to take something from the planet and-"
The Master hits Dooku across the head and seems to shoot him with a gun.
"Your companion is alive Doctor and so is your master, Qui-Gon." The Master said "If you want to see either of them alive, meet with me on Mustafar in exactly three days of this planet."
The Doctor flew his ship in as another was leaving for the planet.

The Doctor asked Obi-Wan and Qui-Gon to pilot and he got out on the side to pursue The Master. He kept his balance as they were flying steady. A door opened from the ship. The Master had Sarah Jane hostage and too far away for him to do anything.
"Doctor, say goodbye to your companion." were the last words The Master said before Sarah Jane was thrown out the ship.