The armada is, in general, a monumental headache for a number of reasons. The basic idea was for Cyclonus to have an group of followers identical to him in design, as a natural counterpart to Scourge's Sweeps. This is evidenced by the description for them given in the movie's script:
- CYCLONUS is CREATED and then his "armada" of similar, but smaller and similarly colored and clad creatures are formed.
However, while the original comic book adaptation of the movie followed through with this intention (in terms of art, if not dialogue), the actual movie itself did anything but. Only one armada robot is shown to be created onscreen, and promptly vanishes from the film mere seconds later, replaced in the group (generally speaking) by a third Sweep.
Consequently, opinions differ on the armada's actual "existence", with some arguing that since Cyclonus's personal army was dropped in production and removed from the film immediately after being introduced, its inclusion is little more than an error, and should be ignored.
Five Faces of Darkness
At least four jets of Cyclonus' design take part in the final assault on Cybertron in "Five Faces of Darkness, Part 5", appearing in a single shot on two occasions. It is a rare thing, however, to find this scene taken seriously, given just how rife with errors the whole mini-series is, although you might have room to argue that if Bombshell were the armada (see below for that mess), then he might still be able to clone himself to produced more armada robots.
Transformers: The Animated Movie
IDW's 2006 Transformers: The Animated Movie comic, a faithful retelling of the 1986 movie, inserts its own "explanation" for what happened to the armada, showing a jet identical to Cyclonus being destroyed by a blast of fire-breath from Grimlock's fire-breath. Although Grimlock did indeed use his fire-breath in this manner in the movie itself, his target was unambiguously Cyclonus himself with Galvatron inside. While Cyclonus survived that encounter with little damage, his lookalike in the comic goes kersplodey with equal unambiguity.
Who is the armada?
The armada's identity prior to re-creation somewhat fraught, tied up as it is with the question of who Cyclonus is. In the finished film, Bombshell is shown being transformed into Cyclonus by Unicron, while Skywarp becomes the solitary armada robot. But, some fans reason, if the armada promptly disappears and is replaced with a Sweep, then the animation of the recreation scene is erroneous. This, then, opens up the scene to interpretation, and has left a lot of fans asking who actually became the one true Cyclonus—Bombshell or Skywarp? As a knock-on effect of that, the identity of the armada is also called into question—even though it is a fairly pointless question, since, if the armada does actually exist, then there's no problem, and no reason to question the visuals, beyond an obstinate desire on the behalf of the person doing the questioning for their preference to be "true."
Confusion of the matter aside, the vast preponderance of subsequent sources simply agree with the visuals of the recreation scene as depicted in the movie, showing Cyclonus to be created from Bombshell, and the armada to have been made from Skywarp. IDW's movie adaptation does so, and BotCon's Universe comics feature Cyclonus and Skywarp existing side-by-side, inferring that the armada was Skywarp and was eventually changed back to his original form. Additionally, the 2007 Masterpiece Skywarp toy includes an 'Armada Decepticon' sticker which seems to indicate Skywarp did indeed become the armada.
There are some pieces of nominally official material that go the other route—most prominently, the profiles written by Australian fans for the 2003 Madman Entertainment DVD release of the movie, later used on several UK Metrodome DVDs, which state with complete unambiguity that Skywarp became Cyclonus. Generally speaking, no one really takes this seriously, since it's obvious it was written by a fan who was pushing their interpretation of the matter, and not proof-read by anyone who would dispute it.
This may all be moot; everyone but Megatron involved in Unicron's re-creation appears to have been dead, so neither Cyclonus nor his Armada should remember their previous existence any more than Hook, Line, and Sinker do. Notably, both Cyclonus's Marvel Comics Transformers Universe profile and his Heroes of Cybertron bio actually state that he was forged from the remains of several Decepticons.