The Mother-Hen Ship's third and final battle introduces a new attack in its sixth phase where it fires a stream of neutron bolts towards the player's ship periodically. The bolts move so fast that it caught many new players off-guard, not helped by the fact that the boss sends even more chickens to shore up its defenses the moment it starts using the stream attack.
Its 3's incarnation also appears in Universe. It was another easy early game boss in 3, with its only attack being its rings of neutron bolts. However, said ring attack in Universe fires even more bolts per ring than 2 and 3 when on higher difficulties, which can reach Bullet Hell levels and shorter gaps in its rings as a result.
Chicken Invaders 3: Revenge of the Yolk
The Mysterious Ship's attack involves firing a cross of lasers as it moves around the screen, which are fired without warning. Memorising its lasers and keeping track of its movements is a must to ensure you do not get caught in its crossfire. And hope it doesn't move towards the bottom of the screen...
Even worse in Universe as the delays in its lasers can be much shorter. Later updates has it possible to run into one that fires five or six lasers. Fortunately, it does warn the player how many lasers it will use for its attack, but that does not help that experienced players are so used to fighting it with four lasers...
The Yolk Star's first phase has fires four downward-facing lasers at random intervals. What makes it hard is that while the laser cannons do make a charging sound when they are about to fire, it's impossible to tell which laser cannon is about to fire, so the safest way to avoid the lasers is not standing directly under the cannons. It doesn't help that everytime it loses 25% of its HP, terminator enemies, chickens that appear from any side of the screen and try to crash towards the player's ship, come to assist it, making avoiding its lasers even more difficult. Then in its second and final phase, the yolk core tries to ram towards you.
It returns as one of the possible bosses to encounter in Universe, and harder than ever. It is possible to run into the Yolk Star with seven laser cannons ready, giving you very little room to move. Even worse is that it is possible for its Terminator enemies to consist of tougher enemies such as UFO Chickens and Chickenauts.
Chicken Invaders 4: Ultimate Omelette
The Alien Mothership in Retro Galaxy. What makes it threatening is that it drops its blocky debris when you damage its block parts one by one, which can be a very nasty surprise if you happens to damage a block part right under the boss. Not helped by the fact that dropping its parts has a chance of dropping a power-up or a weapon, which can be infuriating when you need the former due to how the series' firepower system works, meaning that you either have to risk getting it by trying not to touch the debris, or use up a missile to clear the debris. Oh, did we mention that all the blocky debris' hitboxes are square-shaped regardless of the debris' shape, meaning that it is possible to crash into the triangle-shaped debris even if it looks like you're not touching it?
Chicken Multiplicity, which may cross with Goddamned Boss as well. It starts with Super Chicken firing rotating lasers, then splits into the Infinity Chickens from wave 40 when destroyed. They fire energy bolts at random directions, which aren't too hard to deal with, but each of them split into 2 Big Chickens when destroyed, which splits into 2 Chickenauts each, which splits into 4 normal chickens each, and finally 4 chicks each. The difficulty lies in the time needed to destroy each of these chickens.
The Henterprise is no slouch in its third and final confrontation. It can fires huge fireballs in all of its phases except for the final phase, and the chick waves it sends out are replaced with harder to destroy metal-suit chickens. And in its final phase, it fires lasers at random directions, which makes dodging them a mess. note There are safespots in this attack by hugging close to either the leftmost or rightmost side of the screen while nearing the Henterprise, as the lasers can't reach those areas. In Universe however, it is possible for the lasers to be fired at there, invalidating the safespots as a result. Oh, and it is possible to fight it in Universe, and not only it uses its black feather attacks alongside its usual attacks, meaning it can drop black feathers and fire huge fireballs right off the bat, on higher difficulties it attacks much, much faster.
Chicken Invaders Universe
Of all the returning bosses, the third U.C.O. from 3 is considered harder than the final bosses of the previous games themselves (with the exception of the Yolk Star). On higher difficulties, not only it is much harder to take down, it fires even more fast, aimed neutron bolts at your ship point blank, not to mention the possibility of its arms ramming into you. It was so bad that later updates have it appear without its red laser gun on lower difficulties, as well as nerfing its health slightly while many weapons received a buff, though it still instills dread in many players that joined during Early Access when the Boss Subtitles read "Close Encounters... of the Chicken kind!".
In 4 and the early versions of Universe, the Infinity Chickens are much more handleable as they let go bursts of energy bolts fired in random directions periodically for the rest of the fight. Later updates have those bursts to be accompanied by spinning fireballs on higher difficulties, which were usually only used when the bosses stop rotating around the screen, flooding the screen with so many energy bolts and fireballs that make you wish your ship has a tiny hitbox. note It is possible to shrink your hitbox by stacking up to 3 Eggular Repulsors in your ship's slots before starting a mission, but that tactic is considered Awesome, but Impractical
Ditto for the Supernova Core, when it was considered a Breather Boss due to the opportunities of stocking up powerups dropped from its rotating turrets, and its burst of three fast, aimed energy bolts aren't too much of a threat. Come to later updates, the core's burst attack grows in the number of bolts fired in proportion to how many barriers you have destroyed, averting the Breather Boss trope as a result. Better get those bullet misdirection skills ready!
Even the Egg Cannon got in on the buffs as well, for later updates have that every time it enters the next phase, it stops whatever attack it was using and skips straight into the attack that is introduced in said phase immediately, changing the dynamics of the fight as a result. Busy farming powerups by shooting down the endless chicken waves in the first phase while the sinister fanfare plays every time you damage the Egg Cannon into the next phase and happen to be in the way of its laser turrets? Surprise triple laser attack to the face!
The game even introduces the Egg Cannon Cannon Cannon Cannonade, which is memorization-heavy. Its first phase corners you by having its triple laser attack angled towards the center, then if you are in an unfortunate position, you'll get crushed by the beam streak sweep, forcing you to memorize the gaps in its beam sweep. Its second phase has a double beam streak swing towards top and bottom, and don't even think about standing in the center because it can fire a fast, forwarding beam streak at there too. The third phase is where it is the most dangerous, as it fires a burst of high-speed egg arcs that can cause seasoned players to panic as the gaps vary widely, and can fire laser walls, forcing you to move out fast, meaning the heavy bomber spacecraft is screwed against that attack without a projectile-cancelling special weapon in hand.
Magnetic Manipulator is very frustrating to deal with. It can form a rotating ring of asteroids to protect itself, making it harder to take down by forcing you to move out of the ring's way, and its asteroid dropping technique is tricky to dodge. The most dangerous of its attacks, however, is its asteroid waves, which come extremely fast on higher difficulties. And it only appears in Meteor Storm missions, making asteroid belt areas that consist of already That One Wave of asteroids even more difficult.
Bossa Nova, the living supernova core, has a plethora of dangerous attacks at its disposal in addition to being shielded by a ring of supernova debris. It can use its ring of debris to crush you at your position, meaning that if you are too far from it, there will be a high chance that you have no way to escape its ring. It can also summon a wave of supernova debris at you, meaning that you're pretty much screwed at low firepower. And its most dangerous attack, which is indicated by a glowing ring, is that its ring of debris extend all the way to the other end of the screen and then return to the core, and if you can't find an opening when the debris reaches the other side of the screen, hope you have Dimensional Phaseout ready with you...
You think Chicken Multiplicity was bad? Wait until you see Chicken Exponentiality, which is 5's version of Chicken Multiplicity with the fifth game's bosses and Elite Mooks. First the Henperor's Apprentice, which uses a larger forcefield to accomodate for the large screen size, then uses the player ship direction screwing technique and the rotating lasers it retains for the rest of the fight. Then it splits into a Military Chicken and a Party Chicken, and either of them split into three Chick Gatling Guns when destroyed. Said Chick Gatling Guns split into three Armored Chickens when destroyed, which splits into two chickens that split into four chicks that try to ram into your ship when damaged, and said chicks are considered to be even worse than Armored Chickens themselves. At one point, your ship could permanently get stuck in the direction the Henperor's Apprentice put you into for the rest of the fight when it's destroyed, which was luckily patched out.