As Jaune looked at the chancellor's logs, he discovered he was talking to the count. General Grievous also looked at the orders in the chips. He reprograms order 66 and finds that private funds were sent to the Separatist leaders, so he takes his findings to the Jedi council.

Obi-wan: so jaune, what did you find?

Jaune: Yes, the chancellor played both sides. He is using the republic and the cis for his gain to rule this galaxy. I had Kix do some tests on Fives and an unknown substance. drugged him

Anakin: So Fives was right...

Jaune: yes. Also, I looked at the program in the chip and found a set of orders, including order 66 or knight fall.

Obi-wan: wait, this wasn't on the list of orders we received from the chancellor

Jaune: I looked at all the mission reports from the last three years and found that the separatists were ready when the republic was about to do invasions or oversieges. It was him giving our intel all along.

Windo: so how can we arrest him without him giving the order?

Jaune: Order 65 can be worked on, and I can also reprogram the order 66 to something stupid

Windo: whatever it is, do it.

Jaune: yes, sir.

Jaune went to do the reset on order 66, but Anakin went to talk to Jaune.

Anakin: so, jaune, can I ask you something?

Jaune: Sure, what's up, in general?

Anakin: Jaune, how often have I told you to call me Anakin?

Jaune: I'm sorry, Anakin. I used to call all the Jedi by their ranks, so what's up?

Anakin: I and Padme was thinking, and we want you to be the godfather of our kids.

Jaune: what about Rex? He has been there for years.

Anakin: we asked him, and he said to ask you...so what do you say?

Jaune: what do I think? Hell yeah, man.

Anakin: good, now let's deal with this traitor.

Jaune: let's do it.

At the chancellor's office, where Jaune and a group of clones entered the room, Jaune and a squad of clones entered with their weapons aimed at the chancellor.

Jaune: Chancellor Palpatine, you being relieved of duty 

Palpatine: It's treason, then.

Jaune: surrender chancellor 

Palpatine: You are committing mutiny corporal

Jaune: explain your action.

Palpatine: my action?

Jaune: for starting this war and the plot against the Jedi.

Palpatine: oh, that action... I'm surprised you were able to figure it out for a teen

Jaune: surrender, chancellor. Your our number 

then Palpatine force pushed them back 

Palpatine: I won't be undermined by a boy found by clones.

Then, Palpatine jumps out of the office to meet a group of clones.

Clone trooper: get him!!

They all started shooting at him. Palpatine was cutting them down. As Jaune and the others from the office made it down and were about to go after him, Fox came out with his weapon.

Fox: hold it right there.

Jaune: lower weapon fox.

Fox: I can't do that!!

Jaune: I won't ask again!!

Fox: You all traitors!!

Jaune: i used to believe that being a good soldier meant doing everything  they taught you... that is how they enginerd you but your not droids your not programed you have to make your own decisions..

then thorn aimes his weapon at fox and fox aimed back at him.

Thorn: fox don't do it.

then fox lowers his blaster. and other clones pinned him down.

Jaune: take him to lock up.... troopers don't let chancellor palpatine escape.

in the lower city were jaune was with his squad looking for the sith lord.

Jaune: dose anyone has eyes on him?

Clone trooper: no nothing here sir... wait.

then they heard gun fire and lightsaber sounds 

Clone trooper: he is too powerful... hurry ahhh..

then jaune look and saw palpatine cutting down the other squad of shocktroopers and jumps into the buildings.

Jaune: he's coming.

and everyone got ready for him...

Palpatine: ( echos around the buildings..) you should've brought the jedi with you boy... your right i did start this war!!! 

everyone aimed their weapons in the air not knowing where he was as they heard him laugh and some clones in the middle got together then palpatine see this and jumps to them and killing them.

 Palpatine: your were all my pawns!!

Jaune: get him!!

 Palpatine charges at the clones killing them one by one then until jaune jumps at him and pulled out a lightsaber.

( start at 0:09 to 0:42)

https://youtu.be/mksaSGjjpzU

Kieron: jaune you killed the sith lord..

Jaune: it had to be done sir if he was  still alive he would put everyone including the republic at risk so i did what needed to be done...

Apps: i mean damn kid where did you learn to fight with a lightsaber?

Jaune: anakin and ahsoka tained me when i wasn't training with you guys.

Kieron: that's good in all but this is a major blow for the cis with the sith lord dead along with  count dooku and general grievous the cis has no one left in their command structure.

Jaune: that would end this war and i can go home..  to see pyrrha and weiss...

Apps: are you sure that's a good idea... don't get me wrong i want you to be back with your friends and all but they think your dead..

Jaune: i know but i miss them so much..

Hunter: well what every you chose kid we will be there for you kid because your part of this squad.

dark: but one question if this plan didn't work and the chancellor gave the oder what would of happen?

then jaune went up to a clone..

Jaune: trooper execute order 66.

then the clones looked at him and he said.

Clone trooper: so you want the entire clone army to play a game of twister?

dark: i never thought i see jaune reprogram an order and it was the stupidest one of all... you should stop hanging out with apps and the other clones..

Jaune: and were is the fun in that... come on we have to report to the jedi that the sith lord is dead.