The Special Operations campaign in Mental Omega covers various operations throughout the Third Great War and the Mental Omega War from the perspectives of Allied Nations,
Soviet Union,
Epsilon Army, and
Foehn Revolt that serve as side stories to the main plot.
Originally Special Operations were named Covert Operations, which is a throwback to the original Tiberian Dawn expansion of the same name. This explains the inclusion of several missions (especially those added in version 3.3.4) that are in contrast of the title Covert Operations.[1]
Digital Demon

- Main article: Digital Demon
Suppressed repeatedly, the Pacific Front is in danger of disintegration. Before evacuating to a safer place, Norio Tomokawa attempts to help the loyalists recover some of the lost technologies from a base, where a dangerous weapon activated by the Chinese and traitor forces awaits.
Obstinate

- Main article: Obstinate
Yuri's forces have captured Cannes by using Psychic Beacons to control a United States forces regiment in the city. As several K.I. Scientists, who can benefit the Paradox Project's completion, are still in the city, the Allies try to rescue them, and learn a thing or two about their new enemy.
Convergence

- Main article: Convergence
As Norio Tomokawa and his task force attempt to join the counter-attack operations, an Epsilon blockade of the Panama Canal makes it impossible for them to reach the Virgin Islands. To answer the call for help, the heroes of the Allied Nations join forces together to deal with this crisis.
Fullmetal

- Main article: Fullmetal
While Tanya and Norio are fighting in the Amazonia, the Allies deploy another task force in Africa, in order to gather more resources for their quest. An insurgency against Yuri's Epsilon is happening in Angola, where many Oil Refineries are in the hands of PsiCorps and the Scorpion Cell.
Gridlock

- Main article: Gridlock
After losing his Tactical Nuke Silos in the Amazonas Rainforest, Yuri plans to create a makeshift rocket loaded with a nuclear payload, and launch it from a city in South America against the Paradox Engine. Alerted, the surviving American forces from San Juan quickly react to the threat.
Parasomnia

- Main article: Parasomnia
Archetype

- Main article: Archetype
Ten years before the new war, as the moods of Russian people are changing unfavorably for the Allies still residing in Russia's territories after Stalin's defeat, two skilled soldiers arrive at the site of American laboratories in Ukraine, where its habitants begin to abandon the area.
Eclipse

- Main article: Eclipse
The Chinese forces have begun their march through Kagoshima to acquire the technology created by the Japanese Kanegawa Industries. As they are approaching the K.I. facilities, which store prototype Future Tanks, a Pacific Front army stationed there refuses to surrender. A battle is inevitable.
Trophy Hunter

- Main article: Trophy Hunter
With the Russian-Chinese alliance broken, the forces in Europe have engaged in combat. To preserve their strength and prepare for the defense of their critical positions, the Chinese have begun partial evacuation from the European theater. However, the enemy ambushes them in Santander.
Noise Severe

- Main article: Noise Severe
As the day of negotiation approaches, one of the sides requests the release of long-time prisoners captured by the Russians during the times of conflict as one of the conditions. The Russians agree, however, it appears not all involved are keen on releasing the prisoners. Not those controlled by Yuri.
Dawnbreaker

- Main article: Dawnbreaker
After Yuri's location has been pinpointed, the Russian forces remaining on the ground have regrouped and entered their homeland to aid the main force in the final attack. A long hard road through Ural Mountains awaits them, but an Apocalypse construction complex is a chance to make it easier.
Brothers in Arms

- Main article: Brothers in Arms
Taciturn

- Main article: Taciturn
A Chinese agent has found out about the secret that the Russian dominion does not possess additional MIDAS warheads. Distraught with the vision of the Chinese starting an attack on the Russian territories, Yuri orders an assassination of the agent, before he manages to return to his troops.
Fallen Ashes

- Main article: Fallen Ashes
The Soviets are planning a major operation to take complete control of the African territories in Allies' place. Yuri intends to nip their plans in the bud, else it might pose a threat to the next stage of his design. As Yuri prepares to reemerge in Moscow, the Scorpion Cell readies its forces in Morocco.
Blood Rage

- Main article: Blood Rage
The Creation has been struck with a surprise attack during her mission in Kashmir, which made her go berserk once again. Yuri demands she be tranquilized and brought back to recover from the battle between the forces of Epsilon and the Chinese.
Split Seconds

- Main article: Split Seconds
Yuri believes there is more to the Kanegawa Industries' continued involvement in this war than he had previously suspected. When a research complex full of weapons the Epsilon has never seen before is found deep inside the Japanese territories, Yuri sends his forces to investigate.
Nightcrawler

- Main article: Nightcrawler
The Allies' attacks along the west coast of Africa disrupted PsiCorps' attempt to build a Psychic Amplifier in Bissau, forcing Yuri to find an alternative way to take control of the continent. Unluckily for him, the Scorpion Cell still resists his power and the Allies don't stop their attacks.
Survivors

- Main article: Survivors
Time Capsule

- Main article: Time Capsule