Alright, I think I finally understand the story of the Dark Matter trilogy. I've pieced this together using in game stated lore, strategy guides, and obscure shit from old scenes of Japanese Kirby shit.
There are two Dark Matter in this game. Gooey, and Dark Matter. Gooey is completely different from normal Dark Matter in every way, he has two eyes, a mouth, and a happy-go-lucky personality. He's a complete anomaly that goes against everything Dark Matter is supposed to be.
Somehow, Gooey escapes the Dark Matter, and a Dark Matter is sent to find him. Gooey arrives on Pop Star and the Dark matter follows to get him back. There however, Dark Matter is baffled by the actions and behaviors of the natives, as well as the concept of "friends". He doesn't understand it, but he knows it's good and he wants it. So, he possesses Dedede and everything, thinking it makes them friends. He also gets Gooey like he was originally supposed to, which is why hes always kidnapped when you encounter him.
Now, the Dark Matter wasn't supposed to do this, it has a purpose that it is going renegade for. That's why he has the Swordsman disguise, which he probably picked up around Dream Land. This Dark Matter is similar to Gooey in that he's going against the collective. However, unlike Gooey, his intentions aren't pure, and he's not a complete retard who lets himself get caught. His disguise only fails when he's brought to a corner.
Anyways, Kirby removes him and peace is brought back to Pop Star, and he keeps Gooey around as a friend.
Now, first we need to talk about 0. 0 is the creator, father, and ruler of the Dark Matter. Dark Matter is some bizarre substance that can create lifeforms, like some of the minor enemies from Dreamland 3 and 64, Gooey, Miracle Matter, and of course the major Dark Matter. All of these were created by 0. 0 himself is one big eye that can not feel emotion. It's not something it can grasp at all. The fact that some of its creations do go renegade doesn't make sense to it. It somehow could tell that not only did a renegade Dark matter fall at Pop Star, but there's still a renegade Dark Matter there (Gooey). So, 0 brings his entire fleet of Dark Matter and possesses the entire planet.
Now, what Kirby uses to fight the Dark Matter and 0 with is the Love-Love Stick, a holy weapon made of emotions, happiness, and all that fun stuff. You could say that all those positive emotions could be used as a weapon to kill 0, but I don't think that was Kirby's intentions. I think Kirby was trying to get 0 to understand love and emotions, but it was a gambit that ultimately failed since 0 is brutally killed. All Dark Matter is purged from Pop Star. This is Gooey's last appearance, but not the last appearance of Dark Matter, so I don't know if this is where Gooey dies. If it isn't here, then it is in 64 where all Dark Matter is purged from the universe.
02 (Written as 0 Squared, it could be symbolic as oxygen, what life needs to live, or a bitter joke about how squaring 0 is still 0) is brought back, in a different and crippled state. 02 is not just 0 with wings though, they do share one major difference, and that is that 02 can feel emotions. Unfortunately, it's not the ones Kirby intended when using the Love-Love Stick. 02 is only capable of feeling negative emotions like hate, sorrow, abandonment, etc. A being that has never felt any emotions before is now swarmed by negative emotions, and it's probably a massive shift in 02's psyche.
There's no doubt he wants to bring vengeance on the one who did this to him, but he's in a crippled state, and attacking Kirby right after getting killed by him isn't a smart idea. So, 02 decides to conquer other planets to build up the Dark Matter, with the likely plan being to swarm Pop Star when possible. Unfortunately, this goes ariy when on one of the planets a fairy manages to escape and runs to Pop Star.
I still don't know what Miracle Matter is meant to be/represent, (maybe 02's failing ability to create proper Dark Matter?) or 02's final awkward grin before he fights Kirby. However, once Kirby puts an end to 02, that brings an end to all Dark Matter in the universe, bring peace.
There are enemies that have visual motiffs taken from Dark Matter, but aside from that don't really share much else and aren't intended to be proper Dark Matter. Also they don't involve the Dark Matter Trilogy's Director Shinichi anyways.