The timeline in the first post is very cool! Anyway, I have my own theory:
I prefer to exclude all the games that have standalone stories and does not develop the world of Kirby (like Pinball Land and Kirakira, or even Dreamland 1 since it's remade in Superstar) because they can be placed in any point of the timeline with no differences.
(MetaKnightmare, arenas, soul versions etc. are not canon. the only canon thing is the release of Galacta Knight from his seal, by MetaKnight, but it's unrelated with the story of Kirby Superstar - it obviously happend before the destruction of Nova, and the return of Dark Mind's minions with the dimensional mirror. To be precise, I assume that Kirby games are instead just recitation shows in Dreamland, and all the characters, even the bad ones, are instead just friends - as shown in the 100% videos of several games).
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Prologue
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Before any game: On Halcandra many magical artifacts are built. This technology uses the light of the stars in order to work. Nova, the Lor Starcutter, the legendary machies of Air Ride, fountains of dreams etc.
The problem of this technology, is that using the light as source, would create an equal amount of darkness as result. If used right, the artifacts would automatically destroy the darkness and keep an equal balance of darkness and light, but if they are overused, Dark Matter is created.
Still in ancient times, a warrior named Galacta Knight is sealed for unknown reasons. Anyway, he probably is related to MetaKnight, and has some links to how MetaKnight got the Galaxia (his sword).
The first (recent) invasion of Dark Matter happens, and nobody is apparently able to fight them. MetaKnight builds the Halberd and makes up an army to fight Dark Matters, as he noticed that they are able to possess people only if they can scare them.
They fight Dark Matters with no fear, but at the end, they have to face the core of the Dark Star: Zero.
MetaKnight uses dark-based powers, and Zero can't be defeated with darkness, a light based weapon is needed. MetaKnight has the Galaxia, but this is not enough. He is able to make Zero weak and seal him into a chest, but he can't destroy it.
Dark Matter race is destroyed, with the exception of a weak Zero that's just sealed instead.
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Rise of the Hero
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Amazing Mirror: (placed before Dreamland 1 events, when MetaKnight releases Galacta Knight) The Mirror World is a mirrored copy of the real world, and it's on Pop-Star. Dark Mind is Zero's reflection, and to be precise, it's the copy of an ancient Zero who atacked the universe aeons ago, probably involved with the story of Galacta Knight. It's possible that the mirror world was created by Galacta Knight himself, in order to seal Zero's soul forever, and probably in order to make this he sealed himself in another dimension as well.
With the release of Galacta Knight by Metaknight, the dimensional mirror appeared again and Dark Mind was able to attack the world. MetaKnight returned on PopStar and tried to defeat Dark Mind, but he failed and was captured by him.
Dark Mind is different from the dark matters and Zero; he can't posses people, but his power is to clone them using the mirrors. Each mirrored character is like a Dark Matter, and Dark Mind is like Zero.
One of Dark Mind's minion took the shape of MetaKnight and went to the normal world, and attacked Kirby.
Kirby was splitted in 4 copies, for some reason. It's unclear if the 4 kirbys returned into one at the end of the game, but it looks like Kirby has not lost his power from this split... probably the cloned Kirbys were an attempt to create some evil mirrored Kirbys but it failed, and it seems that the clones are still around but they are incomplete, they don't have any personality and they appear only sometimes, doing the same thing that Kirby is doing (Kirby usually plays with them in minigames, or uses them to make strange dances at the end of the levels, if the color of them is not a problem); he doesn't fight often splitted because if the kirbies lose some lives, it's like if the real Kirby lost those lives.
Kirby saved MetaKnight and destroyed Dark Mind using MetaKnight's sword. MetaKnight thought that Kirby would not have been able to defeat Dark Mind without the Galaxia.
Dark Mind is not really defeated, but nobody noticed this... Dark MetaKnight will return to Kirby's World in the future.
Dark Kirby is another failed attempt to clone Kirby and make it evil. It's like the Gooey of the Mirror world, he's a good "dark matter".
Kirby Superstar: (MetaKnight releases Galacta Knight, he did it during his training, frustrated by the fact that he was unable to completely defeat Zero)
Kirby VS Dedede - Dreamland 1 events;
Kirby helps Dynablade;
(After being aware that he's the strongest warrior in the galaxy) MetaKnight is sick of Dedede causing problems to Dreamland and wants to take his place as the king of Dreamland, but Kirby stops him;
Marx uses Nova to gain a lot of power but Nova is destroyed.
Kirby's Adventure: the events of this game are placed after the Revenge of Metaknight and before Milkyway Wishes. After the destruction of the Halberd in the fight with Kirby. MetaKnight wants to challenge him again. Kirby wants to restore the Star Rod, MetaKnight wants to stop Kirby (because he knows that Nightmare would take over the fountain of dreams) but he wants also to help him when he is in dangerous situations, so he gives him some invicible candies, but he also attacks Kirby several times. Near the end of the game, MetaKnight has no choices but to challenge Kirby in another duel: if Kirby was able to beat him (the strongest warrior in the galaxy), he would have left him repair the Star Rod, as he would be able to defeat Nightmare.
Kirby defeated both MetaKnight and Nightmare. Dedede is not a villain in this game, he was just trying to defend Dreamland from Nightmare.
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Dark Matter invasion
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Kirby's Dreamland 2/3/64: (MetaKnight is not present because he's repairing the halberd, that's underwater after Kirby destroyed it).
The first loney Dark Matter attacks Dreamland. In fact, the entire universe is under attack, because the destruction of Nova brought another wave of Dark Matters, and a new Zero.
Dark Matters first attack the potential dangers, then they conquer the planets/stars. They sent some dark matters on various stars to conquer them, but when Kirby destroyed the first Dark Matter, they decided to make a big assault to Pop-Star as it was the most dangerous star (Kirby's Dreamland 3).
During the assault, they tried to conquer Floralia too, and they defeated the former king/queen, but Sectonia defeated the Dark Matters and became the new queen. She was a bad queen and the people of the sky started to make a plan in order to get rid of the new queen.
In Dreamland, Dark Matters manage to contaminate everything and take control over the king. Unfortunatelly, Kirby and Gooey (Gooey is a Dark Matter who tried to possess Kirby, but after entering in his body, he lost his dark personality due to Kirby's pure mind, and became a friend of him) defeated Zero using the power of the positive emotions of the inhabitants of Dreamland, which generated light energy.
Zero was killed, but for unknown reasons, his soul survived and he managed to return; probably he used a magical seed found in Floralia, since his 02 form has something strange inside, like a spiked vine or something...
Dreamland won the war, so the Dark Matters decided to stay away from it... They attacked Ripple Star instead, because during the previous invasion, they discovered another great source of light, potentially very dangerous.
The fairies of Ripple Star didn't knew that the crystal was a very powerful weapon against the Dark Matters, so they tried to hide it, but doing so they lost agains Dark Matters and the whole star was contamined.
Ribbon escaped with the crystal but the Dark Matters followed her, and destroyed it.
Dark Matters are very unfortunate, because Ribbon fell on the Pop-Star, and met Kirby. They tried to stop him again, but it was useless, Kirby managed to destroy the whole Dark Matter army. But, Zero remained hidden, since he knew about Kirby's abilities, and he had no hopes to win agains him.
After finding all the pieces of the crystal, Kirby and his crew discovered that the light of it was able to defeat Dark Matters... in fact, an huge amount of Dark Matters were hidden inside of the Fairy Queen's body, and the crystal was able to find them and purge them with a single beam.
Kirby Defeated Zero again, and the Dark Matters are destroyed, this time for sure. (Kirby used the phone that he used in Amazing Mirror to call a warp star).
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A new era
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Canvas Curse: Drawcha attacks Dreamland, and she's defeated by Kirby. Kirby was helped by someone who drawn a rainbow line on the canvas using the power paintbrush. It's "the player", it's unknow who used the paintbrush in the canon of the game. I assume that was Adeleine, since she helped Kirby in his adventure against Dark Matters, and she is the only magical painter who doesn't appear in the game (aside from the ones who aren't introduced yet).
Squeak Squad: The chest in this game is indeed the old chest where MetaKnight sealed the previous Zero; in fact MetaKnight is the only one who knows about the real content of the chest.
Daroach and the Squeak Squad become friends of Kirby at the end
The Halberd is finally, fully repaired.
Kirby Returns to Dreamland: Magolor uses the power of the Lor Starcutter and the Crown to destroy the universe, but Kirby stops him. I assume that he is dead unless he does any other canon appearance... he appeared in minigames and cameos after this, but I think he's stil dead.
When he overused the power of the Crown, he transformed himself into a sort of Dark Matter, and this is the proof that the use of light power can generate dark matters if used without control.
Mass Attack: Nothing really relevant here, aside from the fact that the Squeaks return for some subquest, confirming themselves as recurring characters (theorically).
Kirby Triple Deluxe: Queen Sectonia is defeated and the seeds of the Dreamstalk are the ones that Zero may have used to reborn in Kirby 64 (because of his tail).
Some of Dark Mind's minions make a return.
Paintra is a boss in this game. It's explained that Paintra and Drawcha are twins, and they were forgotten into a canvas in an ancient studio of an artist. This could be linked to the fact that Adeleine went to Dreamland to study art, and it may be linked with Rainbow Curse's plot as well.
Kirby and the Rainbow Curse: ???
There is a new fairy-like magical painter, nothing else is known yet.
The animal friends may have a role in the game, or they are just random cameos.
Let's see when the game will be out.