By the end of the Machine War, the Armada appeared to ring the entire perimeter of 01, apparently in a dormant, cocoon-like state. When a threat was detected, they deployed multiple weapon systems and appendages in preparation for enemy contact.
Neo and Trinity confronted the Armada as they flew the Logos to 01. The Armada, acting in coordination, immediately launched a devastating barrage of tow bombs at the Logos. Due to his connection to the Source, Neo was able to prematurely detonate a large number of the bombs. However, their sheer number and a squad of Sentinels attacking from the rear overwhelmed Neo's powers, forcing Trinity to fly above the permanent cloud cover to disengage and coast over the Armada into 01.
In The Matrix Resurrections, units of the Armada were deployed in the ongoing Machine Civil War.