Detta förklarades tydligt i pilotavsnittet Agents of SHIELD där de visar en Chitauri neurala länken som Agent Grant Ward befriar från Vanchat i Paris.
Den här S.H.I.E.L.D. bevisblad ger mer information (som trots de många stavfel, verkar vara en officiell artefakt av serien ).
The Chitauri Neural Link is a communication pathway between the Chitauri soldiers and their technology. Neural links are often used to assist, augment, or repair cognitive or sensory-motor functions. They can also be used as a type of mind control and manipulation prostheses. The link connects all Chitauri to each other, to their weapons, and to their vehicles. All information and commands are routed through the Mother Ship which guides the Chitauri forces during their invasion. This makes them a rather formidable fighting force.
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The Chitauri Mother Ship acts as the main communication hub for the invading Chitauri forces. Not only does it allow their soldiers to communicate but also directs them in battle. The Chitauri are of a hive mind, a singular collective of alien cybor-like creatures working as one to overwelm their enemies.
Fury orders Iron Man to intercept a nuclear bomb and dispose of it. Stark takes it to the portal and blows up the Chitauri Mother Ship, severing the link between the Mother Ship and it's army, thus killing all the Chitauri in New York with a immense feedback discharge.