On the surface of Naboo.
After the celebration, the republic sent a lot of their forces to the planet. They were there for protection and to help in cleaning up the battlefield.
While their primary objective was to help Naboo recover, it wasn't what it looked like in action. Instead of cleaning up the droids, they seem to be more focused on searching for something.
Naboo soldiers were helping with the search, moving from place to place instead of moving blindly. They were going through the forest, straight to the parts of Darth Maul's spaceship, clearly aware of the parts' positions. They found the parts in the end because Tony left them there to gather more information from the search group.
Tony: "Come on... That's the third one already. This is getting embarrassing. I still can't figure out how they track these things."
Tony didn't know how the search team kept tracking the parts. He tried to use his telepathic ability to see what they knew but got some interference from the Force. He checked with the midichlorians to try and ask for help but he was refused.
It wasn't that it didn't want to, but that it couldn't do it. Apparently, there was a rule that people can't be telepaths without training. Tony may have practiced in Tatooine but he was nowhere close to mastering the skills.
Tony complained about the rule since he knew that a future Fake Skywalker could do it. The Force couldn't help him though because its creator, G. Lucas, was still in charge. It was only able to give him power because 'that KK woman' left a loophole when she planted a trap to take over the universe from its creator sometime before.
It couldn't help Tony use other powers that needed training because there no more distraction it could use for cover. That loophole was covered after god and the Force used it for Tony. The rules may change in the future but for now, it couldn't be of much help.
The Force was apologetic to his playmate but Tony forgave it. The Force already helped him get some Jedi training. He didn't mind doing the rest of the work himself.
Since Tony couldn't do things the easy way, he decided to got old school. He started investigating and searching for clues.
He knew it wasn't due to the Force because there was no guy 'feeling' things out. The search team based their movements on an electronic device. This made his wonder some more.
As far as he could tell, the parts they found were just solid metals. Even his suit was able to identify its materials. While they didn't look special at all, their size suggested that something could be stored inside. The parts were too smooth and seamless though for a hidden compartment. There's also no layer of paint to covering it. The parts they were looking for were solid metal.
Tony couldn't figure out how they tracked these things. He checked them all with his suits scanners. They weren't just Earth scanners, they were Shi'ar latest scanning equipment. He even did the fine-tuning himself. He made sure that the scanners could detect even the most minute of signals when in a close range. He spared no expense trying to improve the scanners but it still didn't detect any kind of signal from it. He couldn't figure out how they managed to locate the parts of Maul's ship from a distance.
In the end, the only thing he could think of is that there are some kind of tracker or beacon embedded inside the pieces of metal that are using some special quantum technology. Something at even with all the knowledge of the MCU in Quantum Physics combined, he still doesn't have a working theory. The rules of Quantum Physics seems to be different here after all. The only thing he thought possible is that the people of this universe may have developed a way to triangulate the location of a Quantum Entangled particle.
Hearing himself say such a vague idea, he couldn't help but be disappointed with himself. He didn't like how the feeling of not knowing why things are happening. He felt helpless.
He kept sending messages to the main body to hurry up and find out how things work here.
_____
While he didn't have any idea how to avoid getting tracked, he did figure out what the search team is looking for. They were looking for the crystals that were mounted on the parts they tracked.
Tony thought it was just some type of Kyber Crystal that powers the ship instead of a lightsaber. Siths were the only other group he knew that use crystals after all. But thanks to the search teams' pursuit, it became apparent that it wasn't the case.
He had his clones go invisible. They then sneaked into the group to get more details. He didn't hear what these crystals are for but he figured that they were important. The only thing he learned is its name, Stygium.
Seeing as they won't be dropping any more hints, Tony stopped letting them get any more parts. He monitored the tracking devices and monitored their progress. When they got near one of the parts, Tony's clones would start moving them again. They led the search teams into circles until they couldn't take it.
_____
After a few months of hiding and waiting for the heat to die down, the search team finally gave up. They concluded that their trackers weren't working anymore as all devices displayed the same results due to Tony moving it repeatedly.
When they gave up, Tony borrowed one of the trackers to check on them. He wanted to see if the space could be tracked from afar.
He tested it out and learned that it only works for a short-range. The groups who used only found the parts because they close to them. Anything farther than a few dozens of kilometers and they wouldn't be able to track it.
Tony returned the tracker while taking note of the manufacturer.
_____
After making sure that there was no one searching for the ship, Tony started rebuilding the Maul's Spaceship.
He wanted to rebuild it so that he could get a spaceship of his own. He could have had his clones commandeer a spaceship in Tatooine but he didn't like the spaceships over there, they were owned by fugitives after all. They might be well maintained but he was worried about something else. He didn't want to turn on the blacklight and see how nasty the ship would be.
At least Sith's have a lot more discipline. Tony did find torture devices in the ship but they were all neatly stored in a box with folding racks. There is also a room specifically for torturing prisoners but it was also pristine. It showed that Maul took great care of his ship.
Knowing that he would have to rebuild the ship sometime later, Tony left the laser emitters from his suit and a portion of his nanites in Naboo. They were there to transform into extra tools as well as weld things that might have been broken during disassembly.
He didn't think reassembling a ship would need anything special because the movies didn't show any complicated process. Besides, it's not like he was repairing a ship. He was just reassembling a spaceship.
It took a lot more time than when it was disassembled but he was able to put things back into place.
He went to the cockpit and started it up. The lights turned on, showing that he did reassemble the ship properly. The displays started to turn on and the startup monitors started loading. Tony saw this and eventually found out the name of the ship.
Tony: "Scimitar. Kind of aggressive but it works. It's not like I could reveal my identity when using this ship anyway. Looks like I'll be using this for illegal purposes."
Tony already started thinking of what he would do with the ship after learning it could cloak. He would use it to have a clone infiltrate all the planets in the galaxy.
When he started studying in Coruscant, he found out that there was no galactic internet. Information could be transmitted between faraway planets but it wasn't a stable connection. Jamming all sorts of transmission on a planet, like what happened in Naboo, could easily prevent news from getting out of a planet. This lack of information is what Tony wanted to exploit.
When the clone war starts, information would become important. Both the Republic and the Separatists would want more information about the other side. Not only that, but they would also want to restrict the information flowing to the other. Selling information is the most effortless way to earn money by then.
One side of the war, the Separatists, might try to attack him. He didn't care because his clones were disposable. He didn't need to cultivate them like the biological clones and could create as many clones as he wants. He wouldn't be affected by attacks and could retaliate immediately by leaking intel to the other side. They might try to strike again but it would just be an endless cycle and they would eventually give up.
They would try to buy his silence and the whole galaxy would be aware of his reputation. By then, he would be able to earn more money effortlessly.
It may be deplorable working for both sides but it's not like he's the first one who did it. The Sith, Palpatine to be specific, was already controlling both sides. He was just following their lead.
Because he was playing both sides, he could also siphon off more funds from both sides. All the funds he would get is less funds for Palpatine to use. Tony didn't know how much funds the Sith Lord used to build all those Star Destroyers for his Final Order fleet but it must have took a long time to accumulate. Tony wanted to siphon as much money from the guy that he wouldn't even have enough spare funds to even think about creating such a fleet.
______
Imagining what would happen in the future, Tony felt excited. He looked at the Scimitar's controls and went to start its engines.
One press of a button and the engines ignited. He immediately took a seat and held the control stick. He pulled on it and waited for the Scimitar to move.
After waiting for some time, he still didn't see any signs of movement. He thought it was just the because he pulled the stick too lightly and tried to pull on it a little harder. He had just pulled on it a bit more when the ship's engines turned off and he started landing.
Tony: "What's wrong?"
Tony reassembled the ship based on his memory. Even though the parts that were took weren't replaced properly, the nanites which took their places should have worked as a replacement. The parts were just mounting brackets after all and devices that utilize the crystals have separate power lines.
Tony had no idea at all what was happening so he begrudgingly went for the manual. There was a full manual in the Scimitar since the ship is a long-range personal cruiser able to be run by one man.
He got to the manual and had it translated. Then, he triggered the ship's self-diagnosis.
He waited for a while until the ship displayed its status report. A lot of parts of the ship were blinking, displaying their problems that the parts weren't tuned properly. There were all sorts of problems in the propulsions that Tony never encountered in the MCU's spaceships.
Tony created clones and started the fine-tuning. It was a good thing that he was able to start the cloaking again.
_____
AN: Wow people didn't like that Maul is still alive. For those who aren't convinced Maul died because his organs are blasted. I present to you, a certain lightsaber-wielding four-handed cyborg.
In Episode 3, near 1:04, his only body parts that weren't in his head were the heart and lungs. No other organs were inside the green goop. Since a none Force-sensitive Cyborg manage to live like that, I think a Sith could harness the Dark side to survive FOR A BIT. Maul wouldn't last a long time in that dismembered condition, but surviving a few days for a Sith doesn't look impossible, to be honest.
Also, The only force of the Dark Side who remained permanently dead (So Far [ANN: I can't believe I have to add this]) is Count Dooku. That was because he was decapitated. At least Disney is consistent with their stuff in one thing.