TPM-AU(To start with) What if Mace Windu had gone with Obi-Wan and Qui-Gon to Naboo on their return

Chapter 1 - Naboo bound.

Yoda looked at the two Jedi standing opposite them. If the Sith had somehow survived the thousand years since their extinction it was only right that a member of the Council go in person with them to determine the validity of Qui-Gon's claims. Mace had agreed to accompany them to Naboo after he had discussed this mystery with Yoda prior to this meeting. "Alone you will not be on this journey, Master Windu has decided to go with you back to Naboo." the wizened Master Yedi stated.

Ten Days Later.

Yoda emerged from the ship that had conveyed the Council and Supreme Chancellor Palpatine to Naboo. After speaking with Mace he had agreed that Obi-Wan was ready for the position of Jedi Knight for the courage and wisdom he had displayed in his time protecting the Queen while Qui-Gon and Windu had dueled the Sith Lord together. With the Senior Jedi's aid Jinn had been able to slay the powerful darksider. The Supreme Chancellor had requested that Jinn and Windu stay on Naboo to aid and advise the Queen in the rebuilding of the Cities that had been damaged by the Battle Droids. Anakin would commence his training under Qui-Gon once he returned to Coruscant.

The ship was traversing Hyperspace on the long journey back to the Republic Capital, the two Jedi Masters sat opposite each other playing Sabacc, a game that Jinn had long excelled at and one habit which the Senior Jedi lamented when discussing him.

Darth Sidious sat mediating on his rage that his apprentice had fallen in battle, for years the Sith Masters had secretly cultivated pawns and dupes amongst other Dark Side Sects such as the Sorcerors of Tund and the Dathomiri Nightsiders as well as several Dark Side Marauders who frequently clashed with the Jedi and would had welcomed the chance to strike a blow back at them by slaying two Master Jedi.

Why risk being exposed to the Jedi when others could do the work for them with the right encouragement. Two such pawns were Rokur Gepta and Malkar and they had agreed to capture the Jedi Masters and place them in Carbonite in exchange for some minor Dark Side talismans that Sidious had long ago tired of. Organic matter had been supplied to the two to maskerade as the bodies of the two Jedi Masters. When the Republic found the debris of the ship and the clone grown flesh they would assume that the two Jedi were killed in a tragic accident. Once he had destroyed the Jedi he could revive the two and show them that the Sith had won before killing them when their despair was at it's greatest.

Obi-Wan sat staring in space attempting to ease the grief in him by focusing on his exercises. His master was dead and now the council expecting him to train Anakin as his apprentice.

52 Years Later.

Since that fateful day since the apparent deaths of Mace Windu & Qui-Gon Jinn, the Clone Wars ravaged the Galaxy, Anakin Skywalker fell to the Dark Side and aided Palpatine in corrupting or destroying the Jedi. The Galaxy was shrouded in darkness under the reign of the Sith. It took the buried love for a father for his son to destroy the Emperor and Fifteen years of long struggle by the New Republic before Supreme Admiral Pellaeon signed the declaration of peace between the Imperial Remanent and the New Republic.

Malkar sat alone in the darkness, that traitor Pellaeon had betrayed the Emperor - the purest manifestion of the Dark Side that he had ever see by surrending to a pack of weaklings and now the Jedi were on the verge of being reborn thanks to Skywalker. His hatred welled up in him. The crew upon hearing the news had wanted to return to Imperial Space and he had been forced to execute them as traitors to the Empire. He would return to Republic space to hunt down and destroy Skywalker before he punished the Supreme Admiral for his treachery. He would leave the ship within the borders of the former Sith Empire and buy transportation to Coruscant from Nar Shadda.