Lost Legacy and Deserters
Described by Battlekukku XV as an "ancient order of avians aspiring to command the skies, find our fabled homeland, and unlock the mysteries of our forebears," the Battle Bird Armada has long followed a dogma establishing birds as the destined rulers of the sky and all beneath it. This was established by the first Battle Kukkus, who managed to unite about half of their race while the others set out on their own. To achieve their goals, the Battle Birds believed that they first had to locate Babylon Garden, the long lost city of the Armada's supposed ancestors, the ancient Babylonians. It was for this purpose that the Battle Lord attempted to inspire Jet the Hawk to help him find it, as he believed Jet had the skills to do so. Unfortunately Jet's conviction remained unchanged, and the Battle Lord had him imprisoned in the hopes that he would change his mind. (SU: #18, #33, CSE)
This action, however, led the Battle Birds to suffer severe setbacks in their enterprises. Jet escaped the brig, also freeing a mechanic, Wave, and a problematic soldier named Storm, who had both been locked up for unrelated offenses. Together, they decided to get back at the Armada for their treatment and find Babylon Garden first, becoming the deserters known as the Babylon Rogues. The loss of the Rogues cost the Armada its best chance of finding the Garden, and forced the Battle Lord to make it a top priority to reign them in after they fled. While they tried to hunt down the deserters over the following years, the Armada would on occasion find itself being hunted by the Rogues, especially when pursuing an objective of mutual interest. (SU: #20, #30, #33)
Since then, two other birds were also known to have deserted the Armada: Bean the Dynamite and Predator Hawk. Bean was thought to have been "taken out" by the Battle Lord (most likely for his crazy antics), but he actually fled, stealing some Extreme Gear in the process. Predator was a highly skilled soldier in the Armada, who had been promoted after many years of vigorous physical and mental training. Hoping for more freedom, Predator was instead met with even more rules and regulations, while all the added power was passed onto Speedy, simply for being the "heir" to the Armada. Furious, Hawk attacked Speedy, only to be caught & thrown in the brig by Battle Lord for his attempted assault. Fortunately for Predator, he was freed by the Babylon Rogues whom he joined for a time. (StH: #173, #187, SU: #23, #30)
Cocoa Island Conflict
During the Second Robotnik War the Armada leased itself to Dr. Eggman in opes of reuniting their scattered race. This arrangement left them rather behind on current events despite having access to the Eggnet, and prompted them to focus on achieving their own objectives. Establishing a training area on Cocoa Island with their headquarters disguised as a sister island to the main one, the Battle Bird Armada were surprised when Miles "Tails" Prower, Bunnie "Rabbot" D'Coolette, and Antoine D'Coolette landed on the beach. Believing they had been found out by special operatives, and apparently unaware that Tails had previously set up a workshop on the main island, they observed the trio for some time. (SU: #17, #18, #19, CSE)
On Speedy's orders with the Battle Lord's clearance, armed troops landed on the island at night for an ambush, eventually subduing the D'Coolette's as Speedy went after Tails. Tails escaped while Bunnie was taken before the Battle Lord, who mistook her for a member of the Dark Egg Legion. Going along with the mistake, Bunnie learned of the Armada's affiliation with the Eggman Empire, gathering details on their operations. She also found out the Rogues' status as former Armada members before being alerted that Antoine escaped his cell. (SU: #17, #18)
Elsewhere, Armada troopers guarding the Sea Fox were neutralized by Tails with knockout gas, allowing the Fox to investigate their base which he deduced was the third "sister island". He then engaged Armada submersibles in battle, briefly complimenting their technology before defeating them, but not before the Sea Fox was damaged, forcing it to surface. Meanwhile, Speedy and Bunnie both went after Antoine and clashed over who had greater authority, only for the coyote to leap to his believed demise from an escape hatch at the top of the headquarters after being supposedly convinced that Bunnie was a traitor. (SU: #18)
Defeat and Retreat
Tails and Antoine (who had been saved by landing into the Sea Fox when he saw it below him) later infiltrated the base through a tunnel beneath the sea bed and while dispatching the guards, were saved when Bunnie showed up to assist them. In the storage bay, the heroes then confronted Dr. Fukurokov who set his Mole Mech against them, which was destroyed by Tails while the D'Coolette's inflicted significant structural damage to the whole base by attacking key areas of the bay. After rescuing Speedy from Mole Mech's wreckage, the three of them escaped from the damaged fortress as it rose from the ocean and headed away from the island. (SU: #19, #20)
After their retreat, Battlekukku XV accosted Speedy for not informing him Bunnie was a Freedom Fighter and told Dr. Fukurokov that he would have to repair the fortress by himself. XV then decided to renew their efforts to find those who left the Armada--namely the Babylon Rogues-- so they could return to their full strength and defeat the Eggman Empire in order to conquer Mobius and get their revenge on Tails, while seemingly oblivious that the Rogues themselves were following them for a confrontation. (SU: #20)
Some time after their failure at Cocoa Island, a Babylonian energy signature was detected by Dr. Fukurokov, and the Battle Birds headed for the origin point. Arriving in the Gigan Mountains, the Armada then mobilized a large force to investigate the energy source, only to encounter the Babylon Rogues as they emerged from the collapsing ruins underground with the key to Babylon Garden. A standoff followed, where Speedy attempted to convince them to surrender peacefully, but the Rogues thought otherwise and took off in an attempt to escape. Armada troopers then shot at the Rogues furiously from their combat pods, but their blasts were evaded with ease and the Rogues quickly outpaced them, leaving only Speedy and Dr. Fukurokov's Pursuit Drones to give chase. (SU: #33, #34)
As the drones were destroyed in short order, Speedy continued after the Rogues up the mountains alone, until he too was bested by them and about to die for it. By that point, the Battle Lord himself joined the fight, and took down the Rogues with almost no effort, rescuing his son in the process. The Rogues were then were forced back into the Armada with death threats leveled against them (a decision that Speedy strongly opposed but could do nothing about), and they surrendered the key over to the Battle Lord. After explaining how his family knew how to work the device, the Battle Lord activated the key, and it displayed a map showing the exact resting place of the Garden. After Speedy relayed the coordinates with orders to proceed, the Armada readied for battle and made course for it's next destination: New Mobotropolis. (SU: #34)
As the Armada approached the city, recon scouts reported back on it's defensive capabilities, comprising mainly of an AI computer that operated a dome force field generated by nanites. This data allowed Dr. Fukurokov to create a device to bypass the shield that the reinstated Babylon Rogues deployed, starting off a full-fledged invasion. The Battle Birds were soon engaged in the sky by their old foe Tails, along with the Freedom Fighters and "King" Ixis Naugus, as they penetrated New Mobotropolis' perimeter. Though the defenders made a valiant effort in the ensuing dogfight, the Armada prevailed due to it's overwhelming numbers and the Battle Lord's domination of Naugus when he tried to wrest control of their flagship. With the Battle Fortress positioned over Castle Acorn, the Battle Lord gave the order to fire it's main cannon and the Battle Birds succeeded in excavating the Babylon Garden's resting place at the cost of the complete destruction of New Mobotropolis, avenging themselves over their foes and practically achieving their destiny in one fell swoop. (SU: #35)
However, things quickly began to go awry for the Armada soon after. Though the Babylon Garden ascended to the sky, it started to fly off just as the Battle Birds realized they lost contact with the Rogues. In a desperate attempt to keep a hold of their destiny, the Battle Fortress fired anchor lines and tethered the two ships together as the Garden headed for the upper atmosphere. Fearing the worst at being betrayed by the Rouges, the Battle Lord then ordered Speedy to board the Garden and take command of the situation. Instead it continued to deteriorate despite Speedy's efforts, as the Babylon Garden rapidly lost altitude for unknown reasons. With the Battle Fortress still hooked onto their ancestors' relic, the Armada was forced to abandon ship before both vessels crash-landed in the nearby mountains. (SU: #36)
Having their destiny denied to them and suffering another defeat, the Battle Birds swore vengeance, this time against the Babylon Rogues in particular, whose betrayal led to this disastrous turn of events. After such a devastating loss though, they had to first focus on salvaging as much of their resources as possible, and began a hurried evacuation of personnel from the crash site. While doing so, a security patrol discovered Sonic the Hedgehog and Tails spying on the operation, and tried to kill them before they could escape. However, the two made short work of the assault pods and sent the soldiers running before they departed, allowing the Battle Birds to continue their business. (StH: #233, SU: #36)
The Battlebird Armada has very advanced surveillance equipment hidden throughout Cocoa Island that not even trained and experienced Freedom Fighters can spot. In terms of combat technology, they have laser pistols, robotic walkers with laser cannons and flamethrowers, flying pods similar in design to the walkers equipped with the same weapons and one very large, heavy-armored battle robot called the "Mole Mech" that shoots lasers and has a segmented arm held together using electrical currents which is able to overpower personal energy shields. Another piece of their technology is Extreme Gear- hoverboards that can travel at incredible velocities comparable to Sonic the Hedgehog.
They also command armed submersibles equipped with technology that allowed them to escape detection by Tails' Sea Fox, though their torpedo weaponry proved inferior. The cabins of these subs are apparently reinforced enough to allow them to survive even when the frame that provides motion and weaponry is destroyed. Overall their technology seems roughly on par with that of the Republic of Acorn: Bunnie's cybernetics proved superior to their walkers and lasers, but were ill-suited to match their most powerful combat machine, while the sensors on Tails' Sea Fox proved unequal to the cloaking/dampening technology used in Armada subs. They also appeared to have made air ships in the past that are now considered outdated, one of them which became the Babylon Rogues' headquarters.
- The Battle Kukkus: supposed heirs of the Babylonian culture, founders of the Battle Bird Armada, and self-appointed leaders through birthright.
- Doctor Fukurokov: head of the R&D department (and possibly sole member), chief of science and advisor, responsible for most of the armada's gear and equipment
- Drs. Bin and Pin: rumored members of the Battle Bird Armada who may have had a hand in the creation/transformation of Bean the Dynamite. According to one possible origin story, the pair of doctors attempted to make Bean into a living weapon by combining dark magic and science. However, given the many stories circulating around Bean's origins, it is possible that the pair are merely a myth. (CSE)
- Troops: The bulk of the armada's warriors is made up of blue-armored avians, either armed with a rifle or piloting submarines, Battle Walkers or aircrafts at the armada's disposal.
- The Babylon Rogues: a group of deserters who left the Armada for various reasons, usually after earning the ire of the Battle Lord. This group has included:
- The Batte Bird Armada originated in the Game Gear game, Tails Adventure (though in the Japanese version of the game they are called the Battle Kukku Army).
- So far, the Battle Bird Armada has appeared solely in the Sonic Universe comics, save for the Babylon Rogues, Predator Hawk, and Bean the Dynamite, plus a cameo of the Armada's soldiers in the beginning of Issue #233.
- Based on dialogue from StH issues #163, #173, and #187, it is implied that Predator Hawk, Bean the Dynamite, and the Babylon Rogues are deserters from the Battle Bird Armada, and that the Armada developed Extreme Gear technology. The Sonic Universe Blog later revealed that they all have previously been in the Armada and that the Battle Bird Armada's story had been planned for over four years.  
- Though it is heavily implied that the Battle Bird Armada were the first ones to develop Extreme Gear, the only members seen using it so far have been deserters such as Bean the Dynamite and the Babylon Rouges. Extreme Gear was not seen anywhere among the Armada's troopers still in the organization or equipment when they first premiered in Sonic Universe's Tails Adventure arc. This is possibly due to mandates on Sega's part; in story Extreme Gear is implied by Speedy to be outdated.
- While not initially stated so in the actual comic, it was believed the "homeland" that the Battle Bird Armada sought was actually known as the Babylon Garden as stated in the Sonic Universe comic blog.  This was later confirmed true as of Sonic Universe Issue #33 during the Babylon Rising arc.
- Sonic Universe Graphic Novel #5 featured early designs by artists Jon Gray and concepts for the Armada and its members. These concepts included the Armada serving as Eggman's resident forces in the Land of a Million Lights, Battlekukku XV as Speedy's grandfather rather than father and Bean as his grandson as well, and the group's connection to the Dynamite Dux, a nod to the video game of that name. An actual allusion to the game came in The Complete Sonic Comic Encyclopedia, in which Drs. Bin and Pin-the protagonists of the game-are mentioned in connection with one of Bean's possible origin stories.