Dr. Thrax is a ghastly foe to mess with. He specializes in the use of chemical and biological weaponry; he prefers toxins over explosives, and other than Jarmen Kell, all camouflaged units and capabilities are unavailable to this general. While this might make him seem weaker than his explosive and stealthed counterparts, don't underestimate him. His toxins are more than capable of raining on your parade. And by "rain" we're talking toxic acid rain that melts flesh and steel with equal efficiency.
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The toxin rebels are not very good at destroying buildings, but are effective against enemy units, especially infantry. However, toxin rebels can be used after a super weapon strike (when the toxins have cleared) to finish buildings off. The anthrax gamma upgrade is almost essential for this, as anthrax beta doesn't do much (if any) damage to buildings. This tactic can be applied with all three levels of rebel ambush, but if the enemy is well defended within their base, the level three ambush is advised.
Another strategy for the rebel ambush which plays more to the strength of the toxin rebel, is using them to surprise the enemy's attack/defense force. For example, if the Chinese enemy has sent a hoard of battle master tanks to attack you, a rebel ambush could be deployed near the tanks to weaken them and destroy some. This tactic can be used with all three levels of the toxin rebel ambush, but is more effective with more rebels. Also note, if you are ambushing stationary (defense) units of the enemy, an ambush right in the middle of the enemy units is quite effective, as the rebels will attack all the surrounding units. This is not advisable for moving armies though, as the rebels will most likely just be run over and killed before doing substantial damage.