Sir, theres something you have to see
What now captain?
The ARC troopers...
It was all a ruse. The Imperial scouts were supposed to come back. Instead something wrong came back.
A parasite had infected all the members of the ARC troopers who were initally recruited. The parasite most likely coming from the unknown regions. The parasite became attached to all standard issue uniforms and was seen as professionalism when they didnt take off their armour off duty. It was not. This would culminate in an attempted seizure of the ship.
After this coup it would be discovered inside the ARC bunks frozen in carbonite would be the scout team that were supposed to be there instead of the ARC.
(I basically wrote this as a send off for the ARC troopers since ISTs are coming back.)