I should have listened more to Daultay Dofine.
—Nute Gunray after discovering the awful truth.
Learning the truth
The Separatist Leaders were headed to the Mustafar system when Nute Gunray stumbled across a recording for the droid leader Grievous. Gunray's master Darth Sidious explained his new apprentice will kill the leaders. Gunray warned everyone just in time.
After learning the awful truth, the leaders dressed up all of their aides, with the exception of Rune Haako, to look like them. San Hill and Poggle the Lesser did not have anyone to cover for them, so they had to suffer a sad fate. After Darth Vader killed the imposter Nute, which was Rute Gunnay in disguise, then Nute Gunray went to Dac to sign a treaty with Viceroy Aneem.
After Nute sucessfully signed the treaty with Aneem and the others, the CISE went on to help spread peace to the galaxy. Although the droid armies were deactivated, Aneem hired some guards to help out. The CISE was almost destroyed by Danny, fellow bodyguard and Sith Lord, in 43 ABY when he killed all the leaders present on Mustafar except for Aneem, M94-RA-7, and Nemo Gunnay who fled the scene. Aneem warned Gunray, but was told not to do anything due to the safety of the CIS's survival. He later died of an old age in 45 ABY. Aneem promised to keep the CISE running strong, but later passed away after the reformation. Nemo Gunnay and tthe rebuilt M94-RA-7 took over the CISE.