Y/N Was in a meeting with General Ironwood

Y/N: Sir my men and I will remain here in case the Droids come back for another attempt to take the Planet.

Ironwood: Very well Captain I would like to promote you to Commander, but Your Boss is the only one who can do that.
Y/N: I will forward it to... 

Y/N's Holo Comms started to beep

Y/N: Sorry General but it seems Chanceler Palpatine is calling me.

Y/N Turns on his Holo Comm.

Palpatine: Execute Order 66 on both Jedi and the Huntsmen and Huntresses with General Ironwood.

Y/N: Yes, My Lord.

General Ironwood: Captain are you alright?

Y/N: I'm Sorry sir But you and everyone here are marked for termination by Order 66 I'm Sorry.
Y/N and the Clone Pulled out their Blasters and Started shooting the Jedi and At Ironwood.
Ironwood and Team RWBY an JNPR With ACE ops Escaped. 

The Clones Surround Y/N

You all Know that there are still Huntsmen Hutresses and jedi on this Planet. They have all be marked for termination by order 66. Under this Directive any and All Huntsmen huntresses and Jedi are to be Executed for treason against the republic. Any Soldier who Does not Comply with the order will also be Executed For Treason. Understood?!
Clones: Yes sir!

Ruby's and the others side of things

Ruby: Why did Y/N and the Clone start Shooting at us.
Ironwood: They were ordered to By Palpatine

 Hail: What I don't get is why the Jedi are being targeted.

Ironwood: Before Y/N started shooting at me I noticed that he was trying to keep himself from following this Order 66 order.
Ruby: as if he didn't want to do it?
Ironwood: Yes.Like he's being controlled by something.

Fives: I know the What's controlling him
They all turned to see Fives, Echo, Rex,  Obi wan, And Ashoka.
Ruby: Fives what's controlling him

Fives: An Inhibiter chip is controlling him and the others if we can get it out of Him we could get him to order the rest to stand down.
Ruby: If you think it'll work I will do it.
Fives: But first we need some where to remove it from him without the others finding us.

Wiss: My Family's House should work.

Ruby Carrying Y/N and placed him down on a table.

Fives: Step back and let Kix remove Y/N's Chip

Kix Removed Y/N's Inhibiter chip.

Y/N woke up a few minutes after.

Y/N: My head.

Fives: Easey there Y/N.
Y/N: General Ironwood I'm Sorry for what happened back there.

Ironwood: I know you wouldn't willingly shoot me.

Ruby: Can you Order the rest to stop following order 66?
Y/N: I will try.

Time Skip Every Clone on the Planet is at Atlas.

Y/N on MIC and on TV: Brothers, What are we doing? We came here to defend this world from the CIS and we did. But we are now being ordered to kill the People we are Sworn to Protect. I will not take part in it any longer!

Y/N Throws his Blasters on the ground .

Y/N: Who will stand with me?!

All but a few Squads of Clone Did what Y/N Did

Vence: Your all Traitors!

Blazer: No Y/N's Right. 

Vence and the other Squads that didn't drop their weapons were arrested.