Separatist Special Operations Command

The Separatist Special Operations Command, sometimes called SpecOps Command or Seppies Command by Clone troopers, was an organization of elite troops in the Confederacy of Independent Systems's Separatist Droid Army, but sometimes functioned within the CIS navy. The SpecOps command functioned as an elite unit in the Droid Army, and was unknown to the Galactic Republic and a majority of the Separatists. The SpecOps were first created by CIS navy officer named Comoro Marek, uncle of Darth Vader's apprentice, Galen Marek, in 24 BBY to counter the greater strength of the Galactic Republic Special Operations Command. By the end of the Clone Wars, the SpecOps fought in many ground battles and space battles against common clone troopers, and also sea battles on aquatic planets, which inspired the creation of the CIS Flotilla.

Comoro Marek, a human who was the creator of the SpecOps Command, was a senior officer in the CIS navy and was seeking a way to improve the Droid Army, and thought of many different droid model ideas which were put into production by the CIS engineers. He was General Grievous's favorite officer, and funded his projects. It wasn't until shortly before the Invasion of Naboo when he first thought of this. At first, the project was one of the most important military project at the time, and was kept secret from a majority of the CIS, and completely from the Republic. Eventually, as the SpecOps began service, the Confederate officers and units were informed of this.

It wasn't until middle 22 BBY until SpecOps units appeared on the battlefronts across the galaxy. The SpecOps were mostly made up of human elites and droid commandos, but as the need for the SpecOps grew, more units were added to them, such as Jump droids, Aqua droids which later became the main droid of the CIS Flotilla, Flame battle droids, and Magma droids. They were mostly sent on the really hard missions that were too sensitive for standard units, but then were used on many different fronts against regular clones. That was when the Republic found out about this, and tried to teach their Clone Commandos and other Republic SpecOps units on how to fight against Separatist SpecOps, but with the new droid models that Comoro came up with, they couldn't keep up with the training and ended up quitting all together. Eventually, the Republic made about 100 clone troopers that were bred specifically to fight against droid SpecOps, but because of the lack of funds and training the project was soon abandoned.

Separatists SpecOps units were notable for helping kidnap Supreme Chancellor Palpatine during the Battle of Coruscant, when SpecOps Magnaguards killed many clones and broke into the Chancellor's apartment. They also took many key positions during the battle, but it wasn't enough and the CIS still lost. Afterwards, more droids for the SpecOps were put into production, but they didn't get a chance to use them before Order 66 happened.