All Special Ops Troopers wore specialized Sonic Helmets, which were modified to protect them from loud explosions and to pick up vibrations. These helmets as well as special training assisted the troopers in combat against Geonosians, their armor being very resistant to their sonic blasters and they could detect the beating of wings. Some troopers were trained as pilots, being able to quickly translate radar pings and locate Separatist naval ships

On Geonosis, Special Ops Troopers wore clone trooper armor with a yellow and brown color scheme. Many were equipped with backpacks and DC-15S Standard Blasters.

Stealth Special Ops Pilots wore grey Special Ops trooper armor with small red and yellow markings on their helmets. Most Stealth Special Ops Troopers used shoulder armor with the same symbol from the Special Ops troopers on Geonosis.

During the Battle of Cristophsis, General Obi-Wan Kenobi introduced a Stealth ship to evade Trench's sensors. Several Stealth Special Ops troops, led by Commander Blackout, assisted in piloting the Stealth Ship. This episode was an interesting quasi submarine movie that was full of tensions.

Known Special Ops Troopers
- Jet
- Spark
- Blackout

Originally, Special Ops troopers were to be communications specialists. However, this was deemed impractical by the writers of The Clone Wars as characters often simply used their personal comlinks for long-range communications. The design was still implemented in the series by way of turning the communications backpack into a high-power scanning device, which one of Mundi's troops used to detect Geonosian wing vibrations.

This Special Ops clone trooper was a member of the unit assigned under Jedi Master Ki-Adi-Mundi and Commander Jet in the Second Battle of Geonosis. At the opening of the campaign, after Mundi's forces had been shot down by the Geonosians' defenses, he ordered his men to continue on to the Republic staging area. Temporarily lacking air support and needing to reach the landing zone quickly, Mundi decided to take a shortcut through a series of caves. As the group entered the cave, this trooper used his experimental comm gear to detect a wing vibration deeper within. This proved to be their only warning before Geonosian warriors began swarming the Clone troopers, but Mundi pressed them forward to reach the other side. Eventually, with the aid of Clone Flame Troopers, they broke through the Geonosian defense and reinforced the landing zone.

Jet wore Special Operations clone trooper armor that was colored yellow and brown to follow the Geonosis paint scheme. Being a commander, he was equipped with a kama and a pauldron. Once we saw him entering a briefing room together with fellow clone commaders Rex and Cody.