TW: Yep. No, Yoda has not, although he's heard bits and pieces from The Doctor over the years.

Tantive III

It was night by the time the ship dropped out of hyperspace near Coruscant's orbit. Once they dropped out of Hyperspace, they disposed of Maul's body by dropping it out the trash shoot into space. Captain Antilles then ordered the ship brought in to its usual docking bay, where Bail was waiting to escort them to his apartment.

Anakin was currently in the cafeteria, adjusting his lightsaber settings when Obi-Wan walked over to him.

"We're nearing the docking bay, we should head towards the exit ramp," Obi-Wan said and Anakin nodded silently. "Are you alright?"

"I don't know. The Force, it feels…" Anakin trailed off but Obi-Wan understood.

"Different. Lighter almost," Obi-Wan supplied and Anakin nodded. "It's because you killed Maul. You're fulfilling the prophecy Anakin."

"You know I never put much stock in that prophecy," Anakin said with a sigh. "Everyone seems to think that I'm this chosen one, but how can I know for sure?"

"If you're looking at me to have all the answers Anakin, you're looking in the wrong place," Obi-Wan said as he sat down next to Anakin. "I've trained you as best as I could, taught you everything I know, done the best I can to guide you. I wish I had the answers you need, but I do not. What I do know…is you have become a far greater Jedi than I could ever hope to be."

"Master-" Anakin started, feeling unworthy of such praise.

"You are impulsive, and I wish you'd stop being so reckless and be a bit more patient, but I have nothing left to teach you. I am very proud of you," Obi-Wan said with a smile.

Anakin swallowed the lump in his throat. It was everything he had always wanted to hear, ever since he was a small child. And yet, he was unworthy of such praise. He knew it from the visions; he could still clearly see the pain on Obi-Wan's face in his head.

"Master…I've disappointed you," Anakin said, taking Obi-Wan aback. "I haven't been very appreciative of your training. I have been arrogant, and I apologize."

"Anakin, there is nothing to forgive," Obi-Wan assured him. "Shall we join the others?"

Anakin nodded, trying not to let Obi-Wan know what he was feeling. But he was sure at least some of his guilt came flooding through their bond. He just hoped Obi-Wan thought it was about his arrogance.

Not long after, Anakin and Obi-Wan joined Ahsoka, Rex, Yoda, Amy, Rory and Windu in walking down the ramp into the darkened hanger. Bail stood waiting for them, a nearby ship large enough to carry all of them behind him.

"I'm glad you all got here safety. I heard there was trouble on the way?" Bail inquired and the group exchanged a look.

"Let's just say we had an unexpected stowaway. How are things here?" Anakin asked, confused when Bail shot him a look he didn't understand.

"Complicated," Bail said after a moment. "We can discuss it all once we meet up with The Doctor."

"Where is he?" Amy asked, not seeing the Time Lord.

"Back at my apartment. We're going to meet him there now," Bail said as he gestured towards the ship behind him. "Let's go. There's not a moment to waste."

Coruscant

Not long after

In his office, Palpatine paused, closing his eyes and taking a deep breath. After a moment, a sinister smile crossed his face.

"Welcome back Anakin," Palpatine said as his eyes snapped open, revealing a sithy yellow.

Bail's apartment

Later that night

In the living room of Bail's loft apartment, The Doctor took a drink of Alderanian wine before gagging and spitting it back into his cup.

"Nope, still don't like wine," The Doctor said, putting the glass down and R2 beeped at him. "I don't know, this mouth is weird."

Further conversation was interrupted by the sound of a ship landing outside on the landing platform. The Doctor made his way over to it, seeing a ship had landed. The doors opened up and Bail walked out, leading the group of Jedi, Rex and the Ponds out. The Doctor smiled in relief at seeing them as R2 rolled up to Anakin and Ahsoka, beeping happily at them.

"R2," Anakin said, happy to see his old friend. "Hey buddy, I'm glad you're okay."

"He's more than okay. You have a very handy droid there," The Doctor said as he approached.

"Oh he knows it," Ahsoka snarked, smiling slightly as she pat R2's domed head. "Good to see you R2."

"Doctor," Amy said in relief as she approached, throwing her arms around him in a hug.

"Hello Pond, I told you it wouldn't be forever," The Doctor said, returning the hug briefly before releasing her and looking towards Rory. "Rory how's the shoulder?"

"Little stiff but nothing a little rest won't cure," Rory said as he glanced down at his shoulder.

"Rest isn't something we have a lot of," Rex noted and The Doctor turned to him.

"Oh hello, I don't think we've been introduced. I'm The Doctor," The Doctor said as he held out a hand.

"Rex," Rex introduced as he took The Doctor's hand and shook it.

"You're a clone," The Doctor noted as they dropped hands and Rex nodded. "Yet you stand with the Jedi and not your brothers."

"My loyalty is to the Republic, not that madman ordering me to hunt down the Jedi Order. Good soldiers do more than follow orders, they do what's right," Rex said firmly and The Doctor stared at him for a long moment before smiling.

"That they do. Good to have you with us Rex," The Doctor said before glancing at Ahsoka. "And you must be Ahsoka."

"You've heard of me?" Ahsoka asked in surprise.

"I've been doing some research. Former Jedi who was trained by Anakin Skywalker and framed for the bombing of the Jedi Temple. You're rather famous," The Doctor said.

Ahsoka merely nodded, uncomfortable that that was what she was famous for.

"Perhaps we should head inside. I fear it's not safe out here," Bail noted as he glanced around.

"The Senator is right. And I feel we have much to discuss," Windu said grimly.

"That we do," The Doctor nodded, all cheerfulness vanishing from him.

Not long after, they stood in Bail's living room, sitting down on few couches as R2 served some drinks.

"Doctor, know the Chancellor was The Master, how did you?" Palpatine inquired and The Doctor sighed.

"A bunch of things really. There was always this feeling like he was…familiar, but it wasn't until he said something The Master once said that it all fell into place. In that moment, he stopped hiding himself from me and, as I looked into his eyes, I know. It all fell into place then," The Doctor said and a moment of silence passed between them.

"Who is The Master exactly?" Anakin inquired and The Doctor smiled tightly.

"A friend, at first. Then he went mad," The Doctor said sadly. "Time Lords, we have a rite of passage. Children of eight are taken to look into a schism, the pure essence of the universe. Some get inspired. Some run away. But a few like The Master, go mad."

"So which one were you?" Amy asked and The Doctor smiled.

"I ran Pond. And I never stopped," The Doctor said before getting back on track. "The Master delights in chaos, in causing torment. Amy, Rory, do you remember Harrold Saxon?"

"You're joking. He was The Master?" Rory asked in disbelief and The Doctor nodded.

"Shortly before I Regenerated into this body, that version of him became trapped in a time lock that should have taken him back to Gallifrey the day it was destroyed. But somehow he got out, landed on Naboo at least a century ago."

"Why so certain, are you?" Yoda inquired.

"Because that's when things start to change. Small things at first, a political election going in a different direction, a minor piece of legislation passed in the Senate, things like that. But the changes get bigger and bigger, the Republic becomes more corrupt, the Jedi a little too stuck in their ways," The Doctor said and Windu scowled.

"You believe The Master can influence us?" Windu almost challenged The Doctor, who met Windu's gaze evenly.

"Without a doubt. He has an ability, an almost hypnotic like ability to influence people with just his words. Even Jedi wouldn't be completely immune to it," The Doctor said confidently.

"That would explain how Palpatine can command the Senate so easily," Bail mused and The Doctor nodded.

"Anyway, my theory is that The Master landed here a century ago and was somehow recruited by the Sith Master at the time as his apprentice. He used his knowledge of the future to influence certain events and created the Palpatine alias so he could eventually become Supreme Chancellor," The Doctor explained as they all listened to him carefully. "His manipulations truly start a few decades ago, when he began manipulating your life Anakin."

"My life? What are you talking about?" Anakin asked in confusion.

"In the history I know you were born on one of the core worlds. But in this timeline, your grandfather was murdered when your mother was a teenager and she was then kidnapped and sold into slavery," The Doctor explained, looking at Anakin sadly as he stiffened. "I believe The Master was behind this."

"Why would he do that?" Anakin said, trying to control his emotions.

"I believe he did this with the intention of dividing you from the Jedi until you were old enough to have a mind of your own, to question the Jedi code," The Doctor explained. "I also believe that nasty business thirteen years ago with Naboo and the Trade Federation was meant to get you to the Jedi Order, so you could be trained in their ways."

Anakin took a breath, trying to control his emotions. Closing his eyes, he released it all into The Force as everyone else tried to process all this.

"So you're saying that everything that happened Thirteen years ago was about getting Anakin to us?" Obi-Wan inquired.

"I believe so, yes," The Doctor said with a nod.

"Planned this for a long time, The Master has," Yoda noted.

"Just before the Clone Wars…my mother was kidnapped, tortured and eventually killed by a group of Tusken Raiders. I had visions about it for weeks," Anakin spoke up, a terrible thought occurring to him. "Do you think The Master had anything to do with that?"

"I cannot say for certain, but it would be just up his alley. I'm sorry Anakin," The Doctor said remorsefully.

Anakin put a hand over his voice, suddenly filled with so many emotions. He had looked up to Palpatine for so many years, but the whole time he'd been using Anakin as a pawn. Had arranged the death of his grandfather, Master Qui-Gon and possibly even his mother. How many terrible events was Palpatine behind.

Anakin clenched his fists tightly, feeling the rage threaten to burst out of him. But he remembered where that had led him in those visions and so he tried to release it all into The Force. Feeling a hand on his forearm, Anakin looked over, seeing Ahsoka had placed her hand there and was looking at him in concern.

"Master," Ahsoka said softly and he smiled tightly.

"I'm fine Snips," Anakin lied.

From the look on her face, Anakin knew Ahsoka didn't buy it. From the looks everyone else was shooting him, they didn't buy it either. But now wasn't the time.

"You said you had a plan. I'd like to hear it," Anakin said as he turned to The Doctor.

The Doctor nodded, looking over at R2, who had stopped serving drinks. The droid moved a little closer to The Doctor before projecting the image of a building. It took the Jedi and Rex a moment to realize it was a control tower of a local military base on Coruscant They'd all been there multiple times.

"The Master has used these Inhibitor Chips to control the Clones," The Doctor said as he pulled the Chip he had gotten from the dead Clone out. "I've been experimenting with it, seeing if I can find a way to neutralize it."

"And have you?" Windu asked and The Doctor nodded.

"A strong enough sonic pulse - like from my screwdriver - shorts it out," The Doctor said as he put it on a nearby table. "Makes it useless and the Clones should regain their free will."

"We'd still need to do it one at a time," Obi-Wan pointed out.

"Or we can do it all at once," The Doctor said, gesturing to R2's projection of the tower. "That control tower has an emergency broadcast system that can reach the entire planet. If I can send a pulse through that system-"

"You can free the Clones from the Chips," Ahsoka realized and The Doctor nodded.

"Of course it's not that simple. It's heavy guarded, I'd need a small team to get in there," The Doctor explained as R2 stopped the projection.

"Then you'll have it," Rex said immediately. "If you can free my brothers from this madman, it will be an honor to serve under you Sir."

"Thank you Rex, but freeing them will be useless as long as The Master remains in power. He'll need to either be deposed…or killed," The Doctor said, lowering his voice slightly at these words.

"Hmm, like killing, you do not," Yoda noted and The Doctor smiled tightly.

"I despise it old friend. But I fear there is no other way. The Master has become too dangerous and powerful to be held by any prison. I fear not even a single Jedi Master can defeat him," The Doctor confessed and a silence descended on the room.

"The Doctor is right, no single Jedi can defeat The Chancellor," Windu agreed. "I suggest that Master Yoda, Obi-Wan, Anakin and myself confront him tomorrow and do what needs to be done."

"You mean assassinate him," Rory noted.

"It's not the Jedi way," Ahsoka said, her face saying how horrified this was to her.

"Gone, the Jedi are. Destroy Darth Sidious, we must," Yoda said grimly.

"May The Force help us," Obi-Wan sighed, seeming to have aged a century.

"Even if you do defeat The Master, the Jedi will still be seen as traitors," Bail pointed out.

"Not once they see this," The Doctor said, pulling out a datapad. "I still have all the data from The Master's office. I managed to decrypt some coded transmissions between him and several Separatist Leaders, including Dooku and Grievous. More than enough to prove that he was behind the Clone War."

"So we need to find a way to get this to someone we trust who can convince people of the truth. I suggest Senator Amidala," Anakin said immediately and The Doctor and Bail exchanged an uneasy look.

"Do you want to tell them or should I?" The Doctor asked awkwardly.

"Tell us what?" Obi-Wan asked, all of them getting an uneasy feeling.

"The night of the attack on the Jedi Temple, Padme was arrested and charged with treasons," Bail said, to the shock of all of them.

"That's absurd, why would anyone believe that?" Ahsoka asked in shock.

"Because of her medical condition. It makes for a very compelling case that she was in league with the Jedi over their supposed plot to overthrow the Senate," The Doctor explained, shooting a look at Anakin, who paled several shades.

"We believe she was taken for leverage against you Anakin," Bail said gently.

"What is he talking about Skywalker?" Windu said as they all looked at Anakin in confusion.

Anakin was silent for several moments, his mind racing. But he knew he could keep quiet about this. The cat was out of the bag.

"Padme…that is, Senator Amidala and I…" Anakin trailed off, trying to put it into words.

"Master, it's okay," Ahsoka said gently, once more placing her hand on his.

"We know Anakin," Obi-Wan said and Anakin looked up at them sharply.

"You do?" Anakin said in surprise.

"Don't look at me, I didn't say anything," Rex held up his hands defensively.

"Had to, he did not. Good at hiding how you feel about each other, you and the Senator are not," Yoda said, a slight flashing across his face.

Windu had a scowl on his face, clearly the only one besides Amy and Rory who hadn't had a clue about Anakin and Padme. But Anakin paid him no mind, in complete disbelief.

"You never said anything," Anakin shocked.

"You're my Master and she's my friend, why would I?" Ahsoka shrugged.

"You are my brother Anakin. I know I haven't always been the best Master and friend, but I would not betray you like that," Obi-Wan said, looking meaningfully at Anakin.

Anakin merely nodded dumbly, still in utter disbelief. But he still had more to say.

"Thank you Master…but there's more," Anakin took a deep breath, not sure how to say it so he just decided to come out with it. "Padme's pregnant."

For a long moment, the room was completely silent. Obi-Wan and Ahsoka stared at Anakin in a mix of shock and disbelief. A dark look crossed Windu's face as Amy and Rory merely stared in disbelief. Yoda stared at Anakin with an unreadable look on his face.

"How long, known of this have you?" Yoda inquired.

"Only since we returned from rescuing The Chanc -The Master," Anakin quickly corrected himself.

"What was your plan Skywalker, to hope we never found out?" Windu asked harshly and Anakin bowed his head.

"I intended to leave The Order once the War was over," Anakin admitted.

"None of that matters at the moment," Obi-Wan said, overcoming his shock and putting the focus back on what was important. "Anakin, how far along is she?"

"Very. I felt the baby kick the night we came back," Anakin said, unable to help the smile that crossed his face.

"The Master wanted you as his new apprentice. But if he can't have you…" Ahsoka trailed off but they all knew where she was headed.

"He'll go after my child," Anakin said, a pit of dread forming in his stomach.

"We will not allow that to happen Anakin," Amy assured.

"Allow it, we cannot. A Sith of your bloodline, disastrous, that would be," Yoda said with a frown.

"Then it's settled then. Tomorrow, we go after The Master," Windu said firmly.

"We still need to find someone we can trust to look at the information and convince the Senate," Bail pointed out.

"Admiral Yularen," Anakin said after a moment of thought. "He's a good man and has no tolerance for traitors."

"Then it's settled. Tomorrow, the Senator will take my findings to Yularen while the rest of us do our best to free the Clones on the planet and stop The Master," The Doctor noted.

"May The Force be with us all," Windu said grimly.

And now they've all met and are all caught up.

Hope The Doctor's plan makes sense.

I don't think it's too out of character for The Doctor to suggest killing The Master, as he has done things like this in the past in the name of peace and saving lives.